diff --git a/CHANGELOG.md b/CHANGELOG.md
index a157b776..31e38a0f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,15 @@
 # Changelog
 ## [Unreleased]
 
+### Changed
+
+- **Explicit Database Migrations**: Database migrations are no longer applied automatically on open
+  - Opening a database with pending migrations now raises `MigrationRequiredError` with a clear message
+  - New `haiku-rag migrate` command to explicitly apply pending migrations
+  - Version-only updates (no schema changes) are applied silently in writable mode
+  - New `skip_migration_check` parameter on `Store` for tools that need to bypass the check
+  - `Store.migrate()` method returns list of applied migration descriptions
+
 ## [0.26.5] - 2026-01-16
 
 ### Added
diff --git a/docs/cli.md b/docs/cli.md
index 4b733ef5..45bd3374 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -305,6 +305,33 @@ haiku-rag init [--db /path/to/your.lancedb]
 
 This creates the database with the configured settings. **All other commands require an existing database** - they will fail with an informative error if the database doesn't exist.
 
+### Migrate Database
+
+Apply pending database migrations:
+
+```bash
+haiku-rag migrate [--db /path/to/your.lancedb]
+```
+
+When you upgrade haiku.rag to a new version that includes schema changes, the database requires migration. Opening a database with pending migrations will display an error:
+
+```
+Error: Database requires migration from 0.19.0 to 0.26.5. 3 migration(s) pending. Run 'haiku-rag migrate' to upgrade.
+```
+
+Run `haiku-rag migrate` to apply the pending migrations. The command shows which migrations were applied:
+
+```
+Applied 3 migration(s):
+  - 0.20.0: Add 'docling_document_json' and 'docling_version' columns
+  - 0.23.1: Add content_fts column for contextualized FTS search
+  - 0.25.0: Compress docling_document with gzip
+Migration completed successfully.
+```
+
+!!! tip
+    Back up your database before running migrations. While migrations are designed to be safe, having a backup provides peace of mind for production databases.
+
 ### Info
 
 Display database metadata:
diff --git a/docs/python.md b/docs/python.md
index da4b9d71..f04fffc7 100644
--- a/docs/python.md
+++ b/docs/python.md
@@ -18,7 +18,7 @@ async with HaikuRAG("path/to/database.lancedb") as client:
     # Your code here
     pass
 
-# Open in read-only mode (blocks writes, skips upgrades)
+# Open in read-only mode (blocks writes)
 async with HaikuRAG("path/to/database.lancedb", read_only=True) as client:
     results = await client.search("query")  # Read operations work
     # await client.create_document(...)  # Would raise ReadOnlyError
@@ -28,7 +28,10 @@ async with HaikuRAG("path/to/database.lancedb", read_only=True) as client:
     Databases must be explicitly created with `create=True` or via `haiku-rag init` before use. Operations on non-existent databases will raise `FileNotFoundError`.
 
 !!! note
-    Read-only mode is useful for safely accessing databases without risk of modification. It blocks all write operations, skips database upgrades on open, and prevents settings from being saved.
+    Read-only mode is useful for safely accessing databases without risk of modification. It blocks all write operations and prevents settings from being saved.
+
+!!! warning "Database Migrations"
+    When upgrading haiku.rag to a version with schema changes, opening an existing database will raise `MigrationRequiredError`. Run `haiku-rag migrate` to apply pending migrations before using the database. See [CLI Database Management](cli.md#migrate-database) for details.
 
 ## Document Management
 
diff --git a/haiku_rag_slim/haiku/rag/app.py b/haiku_rag_slim/haiku/rag/app.py
index 7952f775..48a31a44 100644
--- a/haiku_rag_slim/haiku/rag/app.py
+++ b/haiku_rag_slim/haiku/rag/app.py
@@ -578,6 +578,26 @@ class HaikuRAGApp:
             await client.vacuum()
         self.console.print("[bold green]Vacuum completed successfully.[/bold green]")
 
+    def migrate(self) -> list[str]:
+        """Run pending database migrations.
+
+        Returns:
+            List of descriptions of applied migrations.
+        """
+        from haiku.rag.store.engine import Store
+
+        store = Store(
+            self.db_path,
+            config=self.config,
+            skip_validation=True,
+            skip_migration_check=True,
+        )
+        try:
+            applied = store.migrate()
+            return applied
+        finally:
+            store.close()
+
     async def create_index(self):
         """Create vector index on the chunks table."""
         async with HaikuRAG(
diff --git a/haiku_rag_slim/haiku/rag/cli.py b/haiku_rag_slim/haiku/rag/cli.py
index fb03aa4d..9f8ac8ee 100644
--- a/haiku_rag_slim/haiku/rag/cli.py
+++ b/haiku_rag_slim/haiku/rag/cli.py
@@ -1,5 +1,6 @@
 import asyncio
 import json
+import sys
 import warnings
 from datetime import datetime
 from importlib.metadata import version
@@ -18,15 +19,25 @@ from haiku.rag.config import (
     set_config,
 )
 from haiku.rag.logging import configure_cli_logging
+from haiku.rag.store.exceptions import MigrationRequiredError
 from haiku.rag.utils import is_up_to_date
 
 # Load environment variables from .env file for API keys and service URLs
 load_dotenv()
 
-cli = typer.Typer(
+_cli = typer.Typer(
     context_settings={"help_option_names": ["-h", "--help"]}, no_args_is_help=True
 )
 
+
+def cli():
+    try:
+        _cli()
+    except MigrationRequiredError as e:
+        typer.echo(f"Error: {e}", err=True)
+        sys.exit(1)
+
+
 # Module-level flags set by callback
 _read_only: bool = False
 _before: datetime | None = None
@@ -65,7 +76,7 @@ def version_callback(value: bool):
         raise typer.Exit()
 
 
-@cli.callback()
+@_cli.callback()
 def main(
     _version: bool = typer.Option(
         False,
@@ -141,7 +152,7 @@ def main(
         pass
 
 
-@cli.command("list", help="List all stored documents")
+@_cli.command("list", help="List all stored documents")
 def list_documents(
     db: Path | None = typer.Option(
         None,
@@ -183,7 +194,7 @@ def _parse_meta_options(meta: list[str] | None) -> dict[str, Any]:
     return result
 
 
-@cli.command("add", help="Add a document from text input")
+@_cli.command("add", help="Add a document from text input")
 def add_document_text(
     text: str = typer.Argument(
         help="The text content of the document to add",
@@ -205,7 +216,7 @@ def add_document_text(
     asyncio.run(app.add_document_from_text(text=text, metadata=metadata or None))
 
 
-@cli.command("add-src", help="Add a document from a file path, directory, or URL")
+@_cli.command("add-src", help="Add a document from a file path, directory, or URL")
 def add_document_src(
     source: str = typer.Argument(
         help="The file path, directory, or URL of the document(s) to add",
@@ -236,7 +247,7 @@ def add_document_src(
     )
 
 
-@cli.command("get", help="Get and display a document by its ID")
+@_cli.command("get", help="Get and display a document by its ID")
 def get_document(
     doc_id: str = typer.Argument(
         help="The ID of the document to get",
@@ -251,7 +262,7 @@ def get_document(
     asyncio.run(app.get_document(doc_id=doc_id))
 
 
-@cli.command("delete", help="Delete a document by its ID")
+@_cli.command("delete", help="Delete a document by its ID")
 def delete_document(
     doc_id: str = typer.Argument(
         help="The ID of the document to delete",
@@ -267,10 +278,12 @@ def delete_document(
 
 
 # Add alias `rm` for delete
-cli.command("rm", help="Alias for delete: remove a document by its ID")(delete_document)
+_cli.command("rm", help="Alias for delete: remove a document by its ID")(
+    delete_document
+)
 
 
-@cli.command("search", help="Search for documents by a query")
+@_cli.command("search", help="Search for documents by a query")
 def search(
     query: str = typer.Argument(
         help="The search query to use",
@@ -297,7 +310,7 @@ def search(
     asyncio.run(app.search(query=query, limit=limit, filter=filter))
 
 
-@cli.command("visualize", help="Show visual grounding for a chunk")
+@_cli.command("visualize", help="Show visual grounding for a chunk")
 def visualize(
     chunk_id: str = typer.Argument(
         help="The ID of the chunk to visualize",
@@ -312,7 +325,7 @@ def visualize(
     asyncio.run(app.visualize_chunk(chunk_id=chunk_id))
 
 
-@cli.command("ask", help="Ask a question using the QA agent")
+@_cli.command("ask", help="Ask a question using the QA agent")
 def ask(
     question: str = typer.Argument(
         help="The question to ask",
@@ -368,7 +381,7 @@ def ask(
     )
 
 
-@cli.command("research", help="Run multi-agent research and output a concise report")
+@_cli.command("research", help="Run multi-agent research and output a concise report")
 def research(
     question: str = typer.Argument(..., help="The research question to investigate"),
     db: Path | None = typer.Option(
@@ -408,14 +421,14 @@ def research(
     )
 
 
-@cli.command("settings", help="Display current configuration settings")
+@_cli.command("settings", help="Display current configuration settings")
 def settings():
     config = get_config()
     app = HaikuRAGApp(db_path=Path(), config=config)
     app.show_settings()
 
 
-@cli.command("init-config", help="Generate a YAML configuration file")
+@_cli.command("init-config", help="Generate a YAML configuration file")
 def init_config(
     output: Path = typer.Argument(
         Path("haiku.rag.yaml"),
@@ -447,7 +460,7 @@ def init_config(
     typer.echo("Edit the file to customize your settings.")
 
 
-@cli.command(
+@_cli.command(
     "rebuild",
     help="Rebuild the database by deleting all chunks and re-indexing all documents",
 )
@@ -485,7 +498,7 @@ def rebuild(
     asyncio.run(app.rebuild(mode=mode))
 
 
-@cli.command("vacuum", help="Optimize and clean up all tables to reduce disk usage")
+@_cli.command("vacuum", help="Optimize and clean up all tables to reduce disk usage")
 def vacuum(
     db: Path | None = typer.Option(
         None,
@@ -497,7 +510,32 @@ def vacuum(
     asyncio.run(app.vacuum())
 
 
-@cli.command("create-index", help="Create vector index for efficient similarity search")
+@_cli.command("migrate", help="Run pending database migrations")
+def migrate(
+    db: Path | None = typer.Option(
+        None,
+        "--db",
+        help="Path to the LanceDB database file",
+    ),
+):
+    app = create_app(db)
+    try:
+        applied = app.migrate()
+        if applied:
+            typer.echo(f"Applied {len(applied)} migration(s):")
+            for desc in applied:
+                typer.echo(f"  - {desc}")
+            typer.echo("Migration completed successfully.")
+        else:
+            typer.echo("No migrations pending. Database is up to date.")
+    except Exception as e:
+        typer.echo(f"Migration failed: {e}")
+        raise typer.Exit(1)
+
+
+@_cli.command(
+    "create-index", help="Create vector index for efficient similarity search"
+)
 def create_index(
     db: Path | None = typer.Option(
         None,
@@ -509,7 +547,7 @@ def create_index(
     asyncio.run(app.create_index())
 
 
-@cli.command("init", help="Initialize a new database")
+@_cli.command("init", help="Initialize a new database")
 def init_db(
     db: Path | None = typer.Option(
         None,
@@ -521,7 +559,7 @@ def init_db(
     asyncio.run(app.init())
 
 
-@cli.command("info", help="Show database info")
+@_cli.command("info", help="Show database info")
 def info(
     db: Path | None = typer.Option(
         None,
@@ -533,7 +571,7 @@ def info(
     asyncio.run(app.info())
 
 
-@cli.command("history", help="Show version history for database tables")
+@_cli.command("history", help="Show version history for database tables")
 def history(
     db: Path | None = typer.Option(
         None,
@@ -557,7 +595,7 @@ def history(
     asyncio.run(app.history(table=table, limit=limit))
 
 
-@cli.command("download-models", help="Download Docling and Ollama models per config")
+@_cli.command("download-models", help="Download Docling and Ollama models per config")
 def download_models_cmd():
     app = HaikuRAGApp(db_path=Path(), config=get_config())
     try:
@@ -567,7 +605,7 @@ def download_models_cmd():
         raise typer.Exit(1)
 
 
-@cli.command("inspect", help="Launch interactive TUI to inspect database contents")
+@_cli.command("inspect", help="Launch interactive TUI to inspect database contents")
 def inspect(
     db: Path | None = typer.Option(
         None,
@@ -586,7 +624,7 @@ def inspect(
     run_inspector(db_path, read_only=_read_only, before=_before)
 
 
-@cli.command("chat", help="Launch interactive chat TUI for conversational RAG")
+@_cli.command("chat", help="Launch interactive chat TUI for conversational RAG")
 def chat(
     db: Path | None = typer.Option(
         None,
@@ -624,7 +662,7 @@ def chat(
     )
 
 
-@cli.command(
+@_cli.command(
     "serve",
     help="Start haiku.rag server. Use --monitor and/or --mcp to enable services.",
 )
diff --git a/haiku_rag_slim/haiku/rag/store/__init__.py b/haiku_rag_slim/haiku/rag/store/__init__.py
index df965f8f..1a7173cf 100644
--- a/haiku_rag_slim/haiku/rag/store/__init__.py
+++ b/haiku_rag_slim/haiku/rag/store/__init__.py
@@ -1,5 +1,5 @@
 from .engine import Store
-from .exceptions import ReadOnlyError
+from .exceptions import MigrationRequiredError, ReadOnlyError
 from .models import Chunk, Document
 
-__all__ = ["Store", "Chunk", "Document", "ReadOnlyError"]
+__all__ = ["Store", "Chunk", "Document", "MigrationRequiredError", "ReadOnlyError"]
diff --git a/haiku_rag_slim/haiku/rag/store/engine.py b/haiku_rag_slim/haiku/rag/store/engine.py
index f0731192..f89acd4e 100644
--- a/haiku_rag_slim/haiku/rag/store/engine.py
+++ b/haiku_rag_slim/haiku/rag/store/engine.py
@@ -14,7 +14,7 @@ from pydantic import Field
 
 from haiku.rag.config import AppConfig, Config
 from haiku.rag.embeddings import get_embedder
-from haiku.rag.store.exceptions import ReadOnlyError
+from haiku.rag.store.exceptions import MigrationRequiredError, ReadOnlyError
 
 logger = logging.getLogger(__name__)
 
@@ -84,6 +84,7 @@ class Store:
         create: bool = False,
         read_only: bool = False,
         before: datetime | None = None,
+        skip_migration_check: bool = False,
     ):
         self.db_path: Path = db_path
         self._config = config
@@ -129,13 +130,12 @@ class Store:
         if before is not None:
             self._checkout_tables_before(before)
 
-        # Run upgrades only on existing databases, set version for new ones
-        # Skip upgrades in read-only mode (they would fail anyway)
-        if not self._read_only:
-            if is_new_db:
+        # Set version for new databases, check migrations for existing ones
+        if is_new_db:
+            if not self._read_only:
                 self._set_initial_version()
-            else:
-                self._run_upgrades()
+        elif not skip_migration_check:
+            self._check_migrations()
 
         # Validate config compatibility after connection is established
         if not skip_validation:
@@ -371,26 +371,55 @@ class Store:
         """Set the initial version for a new database."""
         self.set_haiku_version(metadata.version("haiku.rag-slim"))
 
-    def _run_upgrades(self):
-        """Run pending database upgrades."""
-        try:
-            from haiku.rag.store.upgrades import run_pending_upgrades
+    def _check_migrations(self) -> None:
+        """Check if migrations are pending and error or update version accordingly.
 
-            current_version = metadata.version("haiku.rag-slim")
-            db_version = self.get_haiku_version()
+        Raises:
+            MigrationRequiredError: If migrations are pending.
+        """
+        from haiku.rag.store.upgrades import get_pending_upgrades
 
-            run_pending_upgrades(self, db_version, current_version)
+        current_version = metadata.version("haiku.rag-slim")
+        db_version = self.get_haiku_version()
 
-            self.set_haiku_version(current_version)
-        except Exception as e:
-            # Avoid hard failure on initial connection; log and continue so CLI remains usable.
-            logger.warning(
-                "Skipping upgrade due to error (db=%s -> pkg=%s): %s",
-                self.get_haiku_version(),
-                metadata.version("haiku.rag-slim"),
-                e,
+        pending = get_pending_upgrades(db_version)
+
+        if pending:
+            # Migrations are pending - require explicit migrate command
+            raise MigrationRequiredError(
+                f"Database requires migration from {db_version} to {current_version}. "
+                f"{len(pending)} migration(s) pending. "
+                "Run 'haiku-rag migrate' to upgrade."
             )
 
+        # No pending migrations - update version silently if needed (writable only)
+        if not self._read_only and db_version != current_version:
+            self.set_haiku_version(current_version)
+
+    def migrate(self) -> list[str]:
+        """Run pending database migrations.
+
+        Returns:
+            List of descriptions of applied upgrades.
+
+        Raises:
+            ReadOnlyError: If the store is in read-only mode.
+        """
+        self._assert_writable()
+
+        from haiku.rag.store.upgrades import run_pending_upgrades
+
+        db_version = self.get_haiku_version()
+        current_version = metadata.version("haiku.rag-slim")
+
+        applied = run_pending_upgrades(self, db_version)
+
+        # Update version after successful migration
+        if applied or db_version != current_version:
+            self.set_haiku_version(current_version)
+
+        return applied
+
     def get_haiku_version(self) -> str:
         """Returns the user version stored in settings."""
         settings_records = list(
diff --git a/haiku_rag_slim/haiku/rag/store/exceptions.py b/haiku_rag_slim/haiku/rag/store/exceptions.py
index 4d5c7e7c..a811b5c4 100644
--- a/haiku_rag_slim/haiku/rag/store/exceptions.py
+++ b/haiku_rag_slim/haiku/rag/store/exceptions.py
@@ -2,3 +2,9 @@ class ReadOnlyError(Exception):
     """Raised when a write operation is attempted on a read-only store."""
 
     pass
+
+
+class MigrationRequiredError(Exception):
+    """Database requires migration. Run 'haiku-rag migrate' to upgrade."""
+
+    pass
diff --git a/haiku_rag_slim/haiku/rag/store/upgrades/__init__.py b/haiku_rag_slim/haiku/rag/store/upgrades/__init__.py
index 83a02b07..fb5f1ab9 100644
--- a/haiku_rag_slim/haiku/rag/store/upgrades/__init__.py
+++ b/haiku_rag_slim/haiku/rag/store/upgrades/__init__.py
@@ -1,10 +1,12 @@
 import logging
 from collections.abc import Callable
 from dataclasses import dataclass
+from typing import TYPE_CHECKING
 
 from packaging.version import Version, parse
 
-from haiku.rag.store.engine import Store
+if TYPE_CHECKING:
+    from haiku.rag.store.engine import Store
 
 logger = logging.getLogger(__name__)
 
@@ -14,7 +16,7 @@ class Upgrade:
     """Represents a database upgrade step."""
 
     version: str
-    apply: Callable[[Store], None]
+    apply: Callable[["Store"], None]
     description: str = ""
 
 
@@ -22,24 +24,31 @@ class Upgrade:
 upgrades: list[Upgrade] = []
 
 
-def run_pending_upgrades(store: Store, from_version: str, to_version: str) -> None:
-    """Run upgrades where from_version < step.version <= to_version."""
+def get_pending_upgrades(from_version: str) -> list[Upgrade]:
+    """Get pending upgrades from the given version.
+
+    Returns:
+        List of Upgrade objects where from_version < upgrade.version,
+        sorted by version in ascending order.
+    """
     v_from: Version = parse(from_version)
-    v_to: Version = parse(to_version)
-
-    # Ensure that tests/development run available code upgrades even if the
-    # installed package version hasn't been bumped to include them yet.
-    if upgrades:
-        highest_step_version: Version = max(parse(u.version) for u in upgrades)
-        if highest_step_version > v_to:
-            v_to = highest_step_version
-
-    # Determine applicable steps
     sorted_steps = sorted(upgrades, key=lambda u: parse(u.version))
-    applicable = [s for s in sorted_steps if v_from < parse(s.version) <= v_to]
+    return [s for s in sorted_steps if v_from < parse(s.version)]
+
+
+def run_pending_upgrades(store: "Store", from_version: str) -> list[str]:
+    """Run upgrades where from_version < step.version.
+
+    Returns:
+        List of descriptions of applied upgrades.
+    """
+    applicable = get_pending_upgrades(from_version)
+
     if applicable:
         logger.info("%d upgrade step(s) pending", len(applicable))
 
+    applied: list[str] = []
+
     # Apply in ascending order
     for idx, step in enumerate(applicable, start=1):
         logger.info(
@@ -51,6 +60,11 @@ def run_pending_upgrades(store: Store, from_version: str, to_version: str) -> No
         )
         step.apply(store)
         logger.info("Completed upgrade %s", step.version)
+        applied.append(
+            f"{step.version}: {step.description}" if step.description else step.version
+        )
+
+    return applied
 
 
 # Import upgrade modules AFTER Upgrade class is defined to avoid circular imports
diff --git a/tests/chat/test_chat_app.py b/tests/chat/test_chat_app.py
index 66e7f7e4..501e527a 100644
--- a/tests/chat/test_chat_app.py
+++ b/tests/chat/test_chat_app.py
@@ -4,7 +4,7 @@ from unittest.mock import AsyncMock, MagicMock, patch
 import pytest
 from typer.testing import CliRunner
 
-from haiku.rag.cli import cli
+from haiku.rag.cli import _cli as cli
 
 runner = CliRunner()
 
diff --git a/tests/store/test_migrations.py b/tests/store/test_migrations.py
new file mode 100644
index 00000000..30ffdd38
--- /dev/null
+++ b/tests/store/test_migrations.py
@@ -0,0 +1,191 @@
+from importlib import metadata
+
+import pytest
+
+from haiku.rag.store import Store
+from haiku.rag.store.exceptions import MigrationRequiredError
+
+
+class TestMigrationRequiredError:
+    def test_migration_required_error_is_exception(self):
+        """MigrationRequiredError should be a subclass of Exception."""
+        assert issubclass(MigrationRequiredError, Exception)
+
+    def test_migration_required_error_can_be_raised(self):
+        """MigrationRequiredError can be raised and caught."""
+        with pytest.raises(MigrationRequiredError) as exc_info:
+            raise MigrationRequiredError("Run 'haiku-rag migrate' to upgrade")
+        assert "migrate" in str(exc_info.value)
+
+
+class TestMigrationCheck:
+    def test_new_database_sets_version(self, temp_db_path):
+        """New database should set the current package version."""
+        store = Store(temp_db_path, create=True)
+        version = store.get_haiku_version()
+        expected = metadata.version("haiku.rag-slim")
+        assert version == expected
+        store.close()
+
+    def test_existing_database_same_version_no_error(self, temp_db_path):
+        """Opening a database with the same version should not error."""
+        store = Store(temp_db_path, create=True)
+        store.close()
+
+        # Re-open - should work without error
+        store = Store(temp_db_path)
+        store.close()
+
+    def test_version_bump_without_pending_migrations_updates_silently(
+        self, temp_db_path
+    ):
+        """When version is outdated but no migrations pending, update version silently."""
+        store = Store(temp_db_path, create=True)
+        # Set an older version that has no pending migrations
+        # (newer than all current upgrade steps)
+        store.set_haiku_version("100.0.0")
+        store.close()
+
+        # Re-open - should update version silently, no error
+        store = Store(temp_db_path)
+        # Version should now be current
+        version = store.get_haiku_version()
+        expected = metadata.version("haiku.rag-slim")
+        assert version == expected
+        store.close()
+
+    def test_pending_migrations_raises_error(self, temp_db_path):
+        """When actual migrations are pending, should raise MigrationRequiredError."""
+        store = Store(temp_db_path, create=True)
+        # Set version to before the first upgrade step
+        store.set_haiku_version("0.19.0")
+        store.close()
+
+        # Re-open should raise
+        with pytest.raises(MigrationRequiredError) as exc_info:
+            Store(temp_db_path)
+        assert "migrate" in str(exc_info.value).lower()
+
+    def test_pending_migrations_read_only_raises_error(self, temp_db_path):
+        """Read-only mode with pending migrations should still raise."""
+        store = Store(temp_db_path, create=True)
+        store.set_haiku_version("0.19.0")
+        store.close()
+
+        with pytest.raises(MigrationRequiredError):
+            Store(temp_db_path, read_only=True)
+
+    def test_read_only_version_bump_without_migrations_ok(self, temp_db_path):
+        """Read-only mode with version bump but no migrations should work."""
+        store = Store(temp_db_path, create=True)
+        # Set a version newer than all upgrade steps
+        store.set_haiku_version("100.0.0")
+        store.close()
+
+        # Read-only open should work (version not updated, but no error)
+        store = Store(temp_db_path, read_only=True)
+        # Version should stay at the old value (can't update in read-only)
+        assert store.get_haiku_version() == "100.0.0"
+        store.close()
+
+    def test_skip_migration_check_bypasses_error(self, temp_db_path):
+        """skip_migration_check=True should bypass migration error."""
+        store = Store(temp_db_path, create=True)
+        store.set_haiku_version("0.19.0")
+        store.close()
+
+        # Open with skip_migration_check should work
+        store = Store(temp_db_path, skip_migration_check=True)
+        # Version should remain old (no auto-migration)
+        assert store.get_haiku_version() == "0.19.0"
+        store.close()
+
+
+class TestMigrateMethod:
+    def test_migrate_applies_pending_upgrades(self, temp_db_path):
+        """Store.migrate() should apply pending upgrades and update version."""
+        store = Store(temp_db_path, create=True)
+        store.set_haiku_version("0.19.0")
+        store.close()
+
+        # Open with skip_migration_check to avoid error
+        store = Store(temp_db_path, skip_migration_check=True)
+        old_version = store.get_haiku_version()
+        assert old_version == "0.19.0"
+
+        # Run migration
+        applied = store.migrate()
+
+        # Should have applied migrations
+        assert len(applied) > 0
+
+        # Version should be updated
+        new_version = store.get_haiku_version()
+        expected = metadata.version("haiku.rag-slim")
+        assert new_version == expected
+        store.close()
+
+    def test_migrate_returns_applied_upgrades(self, temp_db_path):
+        """Store.migrate() should return list of applied upgrade descriptions."""
+        store = Store(temp_db_path, create=True)
+        store.set_haiku_version("0.19.0")
+        store.close()
+
+        store = Store(temp_db_path, skip_migration_check=True)
+        applied = store.migrate()
+
+        # Should return descriptions of applied upgrades
+        assert isinstance(applied, list)
+        for item in applied:
+            assert isinstance(item, str)
+        store.close()
+
+    def test_migrate_with_no_pending_returns_empty(self, temp_db_path):
+        """Store.migrate() with no pending migrations returns empty list."""
+        store = Store(temp_db_path, create=True)
+        # Already at current version
+        store.close()
+
+        store = Store(temp_db_path, skip_migration_check=True)
+        applied = store.migrate()
+        assert applied == []
+        store.close()
+
+    def test_migrate_raises_read_only_error(self, temp_db_path):
+        """Store.migrate() should raise ReadOnlyError in read-only mode."""
+        from haiku.rag.store.exceptions import ReadOnlyError
+
+        store = Store(temp_db_path, create=True)
+        store.set_haiku_version("0.19.0")
+        store.close()
+
+        store = Store(temp_db_path, skip_migration_check=True, read_only=True)
+        with pytest.raises(ReadOnlyError):
+            store.migrate()
+        store.close()
+
+
+class TestGetPendingUpgrades:
+    def test_get_pending_upgrades_returns_list(self):
+        """get_pending_upgrades() should return a list of Upgrade objects."""
+        from haiku.rag.store.upgrades import get_pending_upgrades
+
+        pending = get_pending_upgrades("0.19.0")
+        assert isinstance(pending, list)
+        # Should have at least the v0.20.0 upgrade
+        assert len(pending) > 0
+
+    def test_get_pending_upgrades_from_current_version_is_empty(self):
+        """get_pending_upgrades() from current version should be empty."""
+        from haiku.rag.store.upgrades import get_pending_upgrades
+
+        current = metadata.version("haiku.rag-slim")
+        pending = get_pending_upgrades(current)
+        assert pending == []
+
+    def test_get_pending_upgrades_from_future_version_is_empty(self):
+        """get_pending_upgrades() from a future version should be empty."""
+        from haiku.rag.store.upgrades import get_pending_upgrades
+
+        pending = get_pending_upgrades("100.0.0")
+        assert pending == []
diff --git a/tests/test_app.py b/tests/test_app.py
index 7e794e6a..f697afdf 100644
--- a/tests/test_app.py
+++ b/tests/test_app.py
@@ -602,3 +602,74 @@ async def test_rebuild_empty_database(tmp_path, monkeypatch):
 
     calls = [str(c) for c in mock_print.call_args_list]
     assert any("No documents found" in c for c in calls)
+
+
+def test_migrate_with_pending_migrations(tmp_path):
+    """Test migrate method when migrations are applied."""
+    from haiku.rag.store.engine import Store
+
+    db_path = tmp_path / "test.lancedb"
+    store = Store(db_path, create=True)
+    store.close()
+
+    app = HaikuRAGApp(db_path=db_path)
+
+    with patch("haiku.rag.store.engine.Store") as mock_store_class:
+        mock_store = MagicMock()
+        mock_store.migrate.return_value = ["Migration 1", "Migration 2"]
+        mock_store_class.return_value = mock_store
+
+        result = app.migrate()
+
+        mock_store_class.assert_called_once_with(
+            db_path,
+            config=app.config,
+            skip_validation=True,
+            skip_migration_check=True,
+        )
+        mock_store.migrate.assert_called_once()
+        mock_store.close.assert_called_once()
+        assert result == ["Migration 1", "Migration 2"]
+
+
+def test_migrate_no_pending_migrations(tmp_path):
+    """Test migrate method when no migrations are pending."""
+    from haiku.rag.store.engine import Store
+
+    db_path = tmp_path / "test.lancedb"
+    store = Store(db_path, create=True)
+    store.close()
+
+    app = HaikuRAGApp(db_path=db_path)
+
+    with patch("haiku.rag.store.engine.Store") as mock_store_class:
+        mock_store = MagicMock()
+        mock_store.migrate.return_value = []
+        mock_store_class.return_value = mock_store
+
+        result = app.migrate()
+
+        mock_store.migrate.assert_called_once()
+        mock_store.close.assert_called_once()
+        assert result == []
+
+
+def test_migrate_closes_store_on_exception(tmp_path):
+    """Test migrate method closes store even if migration fails."""
+    from haiku.rag.store.engine import Store
+
+    db_path = tmp_path / "test.lancedb"
+    store = Store(db_path, create=True)
+    store.close()
+
+    app = HaikuRAGApp(db_path=db_path)
+
+    with patch("haiku.rag.store.engine.Store") as mock_store_class:
+        mock_store = MagicMock()
+        mock_store.migrate.side_effect = Exception("Migration error")
+        mock_store_class.return_value = mock_store
+
+        with pytest.raises(Exception, match="Migration error"):
+            app.migrate()
+
+        mock_store.close.assert_called_once()
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 3f7bef08..01f02582 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -2,7 +2,9 @@ from unittest.mock import AsyncMock, MagicMock, patch
 
 from typer.testing import CliRunner
 
-from haiku.rag.cli import cli
+from haiku.rag.cli import _cli as cli
+from haiku.rag.cli import cli as cli_wrapper
+from haiku.rag.store.exceptions import MigrationRequiredError
 
 runner = CliRunner()
 
@@ -386,3 +388,63 @@ def test_add_document_src_directory(tmp_path):
         mock_app_instance.add_document_from_source.assert_called_once()
         call_args = mock_app_instance.add_document_from_source.call_args
         assert call_args[1]["source"] == str(test_dir)
+
+
+def test_migrate_with_applied_migrations():
+    """Test migrate command when migrations are applied."""
+    with patch("haiku.rag.cli.HaikuRAGApp") as mock_app:
+        mock_app_instance = MagicMock()
+        mock_app_instance.migrate.return_value = [
+            "Add full-text search index",
+            "Add metadata column",
+        ]
+        mock_app.return_value = mock_app_instance
+
+        result = runner.invoke(cli, ["migrate"])
+
+        assert result.exit_code == 0
+        mock_app_instance.migrate.assert_called_once()
+        assert "Applied 2 migration(s)" in result.output
+        assert "Add full-text search index" in result.output
+        assert "Add metadata column" in result.output
+        assert "Migration completed successfully" in result.output
+
+
+def test_migrate_no_pending_migrations():
+    """Test migrate command when no migrations are pending."""
+    with patch("haiku.rag.cli.HaikuRAGApp") as mock_app:
+        mock_app_instance = MagicMock()
+        mock_app_instance.migrate.return_value = []
+        mock_app.return_value = mock_app_instance
+
+        result = runner.invoke(cli, ["migrate"])
+
+        assert result.exit_code == 0
+        mock_app_instance.migrate.assert_called_once()
+        assert "No migrations pending" in result.output
+        assert "Database is up to date" in result.output
+
+
+def test_migrate_failure():
+    """Test migrate command when migration fails."""
+    with patch("haiku.rag.cli.HaikuRAGApp") as mock_app:
+        mock_app_instance = MagicMock()
+        mock_app_instance.migrate.side_effect = Exception("Migration failed")
+        mock_app.return_value = mock_app_instance
+
+        result = runner.invoke(cli, ["migrate"])
+
+        assert result.exit_code == 1
+        assert "Migration failed" in result.output
+
+
+def test_cli_wrapper_catches_migration_required_error():
+    """Test that cli() wrapper catches MigrationRequiredError and exits with code 1."""
+    with patch("haiku.rag.cli._cli") as mock_cli:
+        mock_cli.side_effect = MigrationRequiredError(
+            "Database requires migration. Run 'haiku-rag migrate' to upgrade."
+        )
+
+        with patch("sys.exit") as mock_exit:
+            cli_wrapper()
+            mock_exit.assert_called_once_with(1)
diff --git a/tests/test_inspector.py b/tests/test_inspector.py
index 92a6005e..1f9c82b4 100644
--- a/tests/test_inspector.py
+++ b/tests/test_inspector.py
@@ -3,7 +3,7 @@ from unittest.mock import AsyncMock, patch
 import pytest
 from typer.testing import CliRunner
 
-from haiku.rag.cli import cli
+from haiku.rag.cli import _cli as cli
 from haiku.rag.store.models import Document
 
 runner = CliRunner()
diff --git a/tests/test_versioning.py b/tests/test_versioning.py
index a9269ef0..2a302a61 100644
--- a/tests/test_versioning.py
+++ b/tests/test_versioning.py
@@ -72,20 +72,24 @@ def test_new_database_does_not_run_upgrades(monkeypatch, temp_db_path):
     Store(temp_db_path, create=True)
 
 
-def test_existing_database_runs_upgrades(monkeypatch, temp_db_path):
+def test_existing_database_checks_migrations(monkeypatch, temp_db_path):
     Store(temp_db_path, create=True)
 
-    called = {"value": False}
+    from haiku.rag.store import upgrades
 
-    def mark_called(*_args, **_kwargs):
+    called = {"value": False}
+    original_get_pending = upgrades.get_pending_upgrades
+
+    def mark_called(*args, **kwargs):
         called["value"] = True
+        return original_get_pending(*args, **kwargs)
 
     monkeypatch.setattr(
-        "haiku.rag.store.upgrades.run_pending_upgrades",
+        "haiku.rag.store.upgrades.get_pending_upgrades",
         mark_called,
     )
 
-    # Opening an existing database should trigger upgrades
+    # Opening an existing database should check for pending migrations
     Store(temp_db_path)
 
     assert called["value"]