diff --git a/CHANGELOG.md b/CHANGELOG.md
index 282d25c3..ca912af8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -70,6 +70,12 @@
   - Cleaner separation: LLM outputs chunk IDs, citations resolved programmatically
   - `Citation` fields are now required (no defaults) for type safety
 
+### Removed
+
+- **BREAKING: `markdown_preprocessor` Config Option**: Removed the `processing.markdown_preprocessor` configuration option
+  - Use `convert()`, `chunk()`, and `embed_chunks()` primitives for custom processing pipelines
+  - Transform content at any stage before calling `import_document()`
+
 ### Migration
 
 This release requires a database rebuild to populate the new DoclingDocument fields:
diff --git a/docs/configuration/index.md b/docs/configuration/index.md
index af7ab533..2d18adfd 100644
--- a/docs/configuration/index.md
+++ b/docs/configuration/index.md
@@ -119,7 +119,6 @@ processing:
   chunking_tokenizer: "Qwen/Qwen3-Embedding-0.6B"
   chunking_merge_peers: true
   chunking_use_markdown_tables: false
-  markdown_preprocessor: ""
   conversion_options:
     do_ocr: true
     force_ocr: false
diff --git a/docs/configuration/processing.md b/docs/configuration/processing.md
index 89847b37..b3a8fbab 100644
--- a/docs/configuration/processing.md
+++ b/docs/configuration/processing.md
@@ -11,7 +11,6 @@ processing:
   # Chunking configuration
   chunk_size: 256                            # Maximum tokens per chunk
   context_chunk_radius: 0                    # Context radius for chunk expansion
-  markdown_preprocessor: ""                  # Optional preprocessor script
 
   # Converter selection
   converter: docling-local                   # docling-local or docling-serve
@@ -148,39 +147,6 @@ processing:
   context_chunk_radius: 0
 ```
 
-### Markdown Preprocessor
-
-Optionally preprocess Markdown before chunking by pointing to a callable that receives and returns Markdown text. This is useful for normalizing content, stripping boilerplate, or applying custom transformations before chunk boundaries are computed.
-
-```yaml
-processing:
-  # A callable path in one of these formats:
-  # - package.module:func
-  # - package.module.func
-  # - /abs/or/relative/path/to/file.py:func
-  markdown_preprocessor: my_pkg.preprocess:clean_md
-```
-
-!!! note
-    - The function signature should be `def clean_md(text: str) -> str` or `async def clean_md(text: str) -> str`.
-    - If the function raises or returns a non-string, haiku.rag logs a warning and proceeds without preprocessing.
-    - The preprocessor affects only the chunking pipeline. The stored document content remains unchanged.
-
-Example implementation:
-
-```python
-# my_pkg/preprocess.py
-def clean_md(text: str) -> str:
-    # strip HTML comments and collapse multiple blank lines
-    lines = [line for line in text.splitlines() if not line.strip().startswith("<!--")]
-    out = []
-    for line in lines:
-        if line.strip() == "" and (out and out[-1] == ""):
-            continue
-        out.append(line)
-    return "\n".join(out)
-```
-
 ## File Monitoring
 
 Set directories to monitor for automatic indexing:
diff --git a/haiku_rag_slim/haiku/rag/config/models.py b/haiku_rag_slim/haiku/rag/config/models.py
index ed638740..85417591 100644
--- a/haiku_rag_slim/haiku/rag/config/models.py
+++ b/haiku_rag_slim/haiku/rag/config/models.py
@@ -111,7 +111,6 @@ class ConversionOptions(BaseModel):
 class ProcessingConfig(BaseModel):
     chunk_size: int = 256
     context_chunk_radius: int = 0
-    markdown_preprocessor: str = ""
     converter: str = "docling-local"
     chunker: str = "docling-local"
     chunker_type: str = "hybrid"
diff --git a/haiku_rag_slim/haiku/rag/store/repositories/chunk.py b/haiku_rag_slim/haiku/rag/store/repositories/chunk.py
index 0c562628..04ddcd2a 100644
--- a/haiku_rag_slim/haiku/rag/store/repositories/chunk.py
+++ b/haiku_rag_slim/haiku/rag/store/repositories/chunk.py
@@ -1,4 +1,3 @@
-import inspect
 import json
 import logging
 from typing import TYPE_CHECKING, cast
@@ -16,7 +15,6 @@ from lancedb.rerankers import RRFReranker
 
 from haiku.rag.store.engine import DocumentRecord, Store
 from haiku.rag.store.models.chunk import Chunk
-from haiku.rag.utils import load_callable
 
 if TYPE_CHECKING:
     from docling_core.types.doc.document import DoclingDocument
@@ -196,36 +194,10 @@ class ChunkRepository:
         self, document_id: str, document: "DoclingDocument"
     ) -> list[Chunk]:
         """Create chunks and embeddings for a document from DoclingDocument."""
-        # Lazy imports to avoid loading docling during module import
         from haiku.rag.chunkers import get_chunker
-        from haiku.rag.converters import get_converter
 
         chunker = get_chunker(self.store._config)
-
-        # Optionally preprocess markdown before chunking
-        processed_document = document
-        preprocessor_path = self.store._config.processing.markdown_preprocessor
-        if preprocessor_path:
-            try:
-                pre_fn = load_callable(preprocessor_path)
-                markdown = document.export_to_markdown()
-                result = pre_fn(markdown)
-                if inspect.isawaitable(result):
-                    result = await result  # type: ignore[assignment]
-                processed_markdown = result
-                if not isinstance(processed_markdown, str):
-                    raise ValueError("Preprocessor must return a markdown string")
-                converter = get_converter(self.store._config)
-                processed_document = await converter.convert_text(
-                    processed_markdown, name="content.md"
-                )
-            except Exception as e:
-                logger.error(
-                    f"Failed to apply MARKDOWN_PREPROCESSOR '{preprocessor_path}': {e}. Proceeding without preprocessing."
-                )
-                raise e
-
-        chunks = await chunker.chunk(processed_document)
+        chunks = await chunker.chunk(document)
 
         # Build embedding texts with headings prepended for better semantic search
         # The stored content stays raw, but embeddings capture section context
diff --git a/haiku_rag_slim/haiku/rag/utils.py b/haiku_rag_slim/haiku/rag/utils.py
index fc7fd41f..6009e559 100644
--- a/haiku_rag_slim/haiku/rag/utils.py
+++ b/haiku_rag_slim/haiku/rag/utils.py
@@ -1,9 +1,6 @@
-import importlib
-import importlib.util
 import sys
 from importlib import metadata
 from pathlib import Path
-from types import ModuleType
 from typing import TYPE_CHECKING, Any
 
 from packaging.version import Version, parse
@@ -350,52 +347,3 @@ async def is_up_to_date() -> tuple[bool, Version, Version]:
     return running_version >= pypi_version, running_version, pypi_version
 
 
-def load_callable(path: str):
-    """Load a callable from a dotted path or file path.
-
-    Supported formats:
-    - "package.module:func" or "package.module.func"
-    - "path/to/file.py:func"
-
-    Returns the loaded callable. Raises ValueError on failure.
-    """
-    if not path:
-        raise ValueError("Empty callable path provided")
-
-    module_part = None
-    func_name = None
-
-    if ":" in path:
-        module_part, func_name = path.split(":", 1)
-    else:
-        # split by last dot for module.attr
-        if "." in path:
-            module_part, func_name = path.rsplit(".", 1)
-        else:
-            raise ValueError(
-                "Invalid callable path format. Use 'module:func' or 'module.func' or 'file.py:func'."
-            )
-
-    # Try file path first
-    mod: ModuleType | None = None
-    module_path = Path(module_part)
-    if module_path.suffix == ".py" and module_path.exists():
-        spec = importlib.util.spec_from_file_location(module_path.stem, module_path)
-        if spec and spec.loader:
-            mod = importlib.util.module_from_spec(spec)
-            spec.loader.exec_module(mod)
-    else:
-        # Import as a module path
-        try:
-            mod = importlib.import_module(module_part)
-        except Exception as e:
-            raise ValueError(f"Failed to import module '{module_part}': {e}")
-
-    if not hasattr(mod, func_name):
-        raise ValueError(f"Callable '{func_name}' not found in module '{module_part}'")
-    func = getattr(mod, func_name)
-    if not callable(func):
-        raise ValueError(
-            f"Attribute '{func_name}' in module '{module_part}' is not callable"
-        )
-    return func
diff --git a/tests/test_preprocessor.py b/tests/test_preprocessor.py
deleted file mode 100644
index 34339c50..00000000
--- a/tests/test_preprocessor.py
+++ /dev/null
@@ -1,72 +0,0 @@
-from pathlib import Path
-
-import pytest
-
-from haiku.rag.config import Config
-from haiku.rag.converters import get_converter
-from haiku.rag.store.engine import Store
-from haiku.rag.store.models.document import Document
-from haiku.rag.store.repositories.chunk import ChunkRepository
-from haiku.rag.store.repositories.document import DocumentRepository
-
-
-@pytest.mark.parametrize(
-    "is_async, marker",
-    [
-        (False, "MARKER_LINE"),
-        (True, "ASYNC_MARKER"),
-    ],
-)
-@pytest.mark.asyncio
-async def test_markdown_preprocessor_applied_parametrized(
-    is_async: bool, marker: str, tmp_path: Path, temp_db_path: Path
-):
-    """Ensure MARKDOWN_PREPROCESSOR (sync or async) transforms markdown before chunking."""
-    pre_file = tmp_path / ("pre_async.py" if is_async else "pre.py")
-    if is_async:
-        pre_file.write_text(
-            """
-import asyncio
-
-async def add_marker(text: str) -> str:
-    await asyncio.sleep(0)
-    return text + "\\n\\nASYNC_MARKER\\n"
-"""
-        )
-    else:
-        pre_file.write_text(
-            """
-def add_marker(text: str) -> str:
-    return text + "\\n\\nMARKER_LINE\\n"
-"""
-        )
-
-    original_pre = Config.processing.markdown_preprocessor
-    try:
-        Config.processing.markdown_preprocessor = f"{pre_file}:add_marker"
-
-        store = Store(temp_db_path, create=True)
-        chunk_repo = ChunkRepository(store)
-        doc_repo = DocumentRepository(store)
-
-        document = Document(content="Hello world")
-        created_doc = await doc_repo.create(document)
-        assert created_doc.id is not None
-
-        # Stub embeddings to avoid network
-        dim = chunk_repo.embedder._vector_dim
-
-        async def fake_embed(x):  # type: ignore[override]
-            if isinstance(x, list):
-                return [[0.0] * dim for _ in x]
-            return [0.0] * dim
-
-        chunk_repo.embedder.embed = fake_embed  # type: ignore[assignment]
-
-        converter = get_converter(Config)
-        docling = await converter.convert_text(document.content, name="test.md")
-        chunks = await chunk_repo.create_chunks_for_document(created_doc.id, docling)
-
-        assert any(marker in c.content for c in chunks)
-    finally:
-        Config.processing.markdown_preprocessor = original_pre