diff --git a/docs/configuration.md b/docs/configuration.md
index 9e522a44..dadf6015 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -104,10 +104,10 @@ a2a:
 
 ## Programmatic Configuration
 
-When using haiku.rag as a Python library, you can configure it programmatically using `set_config()`:
+When using haiku.rag as a Python library, you can pass configuration directly to the `HaikuRAG` client:
 
 ```python
-from haiku.rag.config import set_config, AppConfig
+from haiku.rag.config import AppConfig
 from haiku.rag.client import HaikuRAG
 
 # Create custom configuration
@@ -117,18 +117,17 @@ custom_config = AppConfig(
     processing={"chunk_size": 512}
 )
 
-# Set the configuration globally
-set_config(custom_config)
-
-# All subsequent operations use this configuration
-client = HaikuRAG(db_path)
+# Pass configuration to the client
+client = HaikuRAG(config=custom_config)
 ```
 
+If you don't pass a config, the client uses the global configuration loaded from your YAML file or defaults.
+
 This is useful for:
 - Jupyter notebooks
 - Python scripts
 - Testing with different configurations
-- Applications that need runtime configuration
+- Applications that need multiple clients with different configurations
 
 ## API Keys
 
diff --git a/src/haiku/rag/client.py b/src/haiku/rag/client.py
index 40b81f0f..b9d4a1b5 100644
--- a/src/haiku/rag/client.py
+++ b/src/haiku/rag/client.py
@@ -8,7 +8,7 @@ from urllib.parse import urlparse
 
 import httpx
 
-from haiku.rag.config import Config
+from haiku.rag.config import AppConfig, Config
 from haiku.rag.reranking import get_reranker
 from haiku.rag.store.engine import Store
 from haiku.rag.store.models.chunk import Chunk
@@ -25,16 +25,23 @@ class HaikuRAG:
 
     def __init__(
         self,
-        db_path: Path = Config.storage.data_dir / "haiku.rag.lancedb",
+        db_path: Path | None = None,
+        config: AppConfig = Config,
         skip_validation: bool = False,
     ):
         """Initialize the RAG client with a database path.
 
         Args:
-            db_path: Path to the database file.
+            db_path: Path to the database file. If None, uses config.storage.data_dir.
+            config: Configuration to use. Defaults to global Config.
             skip_validation: Whether to skip configuration validation on database load.
         """
-        self.store = Store(db_path, skip_validation=skip_validation)
+        self._config = config
+        if db_path is None:
+            db_path = self._config.storage.data_dir / "haiku.rag.lancedb"
+        self.store = Store(
+            db_path, config=self._config, skip_validation=skip_validation
+        )
         self.document_repository = DocumentRepository(self.store)
         self.chunk_repository = ChunkRepository(self.store)
 
@@ -430,7 +437,7 @@ class HaikuRAG:
             List of (chunk, score) tuples ordered by relevance.
         """
         # Get reranker if available
-        reranker = get_reranker()
+        reranker = get_reranker(config=self._config)
 
         if reranker is None:
             # No reranking - return direct search results
@@ -452,18 +459,20 @@ class HaikuRAG:
     async def expand_context(
         self,
         search_results: list[tuple[Chunk, float]],
-        radius: int = Config.processing.context_chunk_radius,
+        radius: int | None = None,
     ) -> list[tuple[Chunk, float]]:
         """Expand search results with adjacent chunks, merging overlapping chunks.
 
         Args:
             search_results: List of (chunk, score) tuples from search.
             radius: Number of adjacent chunks to include before/after each chunk.
-                   Defaults to CONTEXT_CHUNK_RADIUS config setting.
+                   If None, uses config.processing.context_chunk_radius.
 
         Returns:
             List of (chunk, score) tuples with expanded and merged context chunks.
         """
+        if radius is None:
+            radius = self._config.processing.context_chunk_radius
         if radius == 0:
             return search_results
 
@@ -593,7 +602,9 @@ class HaikuRAG:
         """
         from haiku.rag.qa import get_qa_agent
 
-        qa_agent = get_qa_agent(self, use_citations=cite, system_prompt=system_prompt)
+        qa_agent = get_qa_agent(
+            self, config=self._config, use_citations=cite, system_prompt=system_prompt
+        )
         return await qa_agent.answer(question)
 
     async def rebuild_database(self) -> AsyncGenerator[str, None]:
diff --git a/src/haiku/rag/config/__init__.py b/src/haiku/rag/config/__init__.py
index b5717060..e0299a6f 100644
--- a/src/haiku/rag/config/__init__.py
+++ b/src/haiku/rag/config/__init__.py
@@ -40,53 +40,15 @@ __all__ = [
     "load_yaml_config",
     "generate_default_config",
     "load_config_from_env",
-    "set_config",
 ]
 
-
-class ConfigProxy:
-    """Proxy for the global configuration that allows runtime updates."""
-
-    def __init__(self):
-        # Load config from YAML file or use defaults
-        config_path = find_config_file(None)
-        if config_path:
-            yaml_data = load_yaml_config(config_path)
-            self._config = AppConfig.model_validate(yaml_data)
-        else:
-            self._config = AppConfig()
-
-    def __getattr__(self, name):
-        """Proxy attribute access to the underlying config."""
-        return getattr(self._config, name)
-
-    def set(self, config: AppConfig) -> None:
-        """Replace the current configuration."""
-        self._config = config
-
-
-# Create the global Config instance
-Config = ConfigProxy()
+# Load config from YAML file or use defaults
+config_path = find_config_file(None)
+if config_path:
+    yaml_data = load_yaml_config(config_path)
+    Config = AppConfig.model_validate(yaml_data)
+else:
+    Config = AppConfig()
 
 # Check for deprecated .env file
 check_for_deprecated_env()
-
-
-def set_config(config: AppConfig) -> None:
-    """Set the global configuration programmatically.
-
-    This allows library users to configure haiku.rag without needing
-    a YAML file or environment variables.
-
-    Args:
-        config: The AppConfig instance to use globally.
-
-    Example:
-        >>> from haiku.rag.config import set_config, AppConfig
-        >>> custom_config = AppConfig(
-        ...     qa={"provider": "openai", "model": "gpt-4o"},
-        ...     embeddings={"provider": "voyage", "model": "voyage-3"}
-        ... )
-        >>> set_config(custom_config)
-    """
-    Config.set(config)
diff --git a/src/haiku/rag/embeddings/__init__.py b/src/haiku/rag/embeddings/__init__.py
index 97c20341..17e85a3e 100644
--- a/src/haiku/rag/embeddings/__init__.py
+++ b/src/haiku/rag/embeddings/__init__.py
@@ -1,17 +1,23 @@
-from haiku.rag.config import Config
+from haiku.rag.config import AppConfig, Config
 from haiku.rag.embeddings.base import EmbedderBase
 from haiku.rag.embeddings.ollama import Embedder as OllamaEmbedder
 
 
-def get_embedder() -> EmbedderBase:
+def get_embedder(config: AppConfig = Config) -> EmbedderBase:
     """
     Factory function to get the appropriate embedder based on the configuration.
+
+    Args:
+        config: Configuration to use. Defaults to global Config.
+
+    Returns:
+        An embedder instance configured according to the config.
     """
 
-    if Config.embeddings.provider == "ollama":
-        return OllamaEmbedder(Config.embeddings.model, Config.embeddings.vector_dim)
+    if config.embeddings.provider == "ollama":
+        return OllamaEmbedder(config.embeddings.model, config.embeddings.vector_dim)
 
-    if Config.embeddings.provider == "voyageai":
+    if config.embeddings.provider == "voyageai":
         try:
             from haiku.rag.embeddings.voyageai import Embedder as VoyageAIEmbedder
         except ImportError:
@@ -20,16 +26,16 @@ def get_embedder() -> EmbedderBase:
                 "Please install haiku.rag with the 'voyageai' extra: "
                 "uv pip install haiku.rag[voyageai]"
             )
-        return VoyageAIEmbedder(Config.embeddings.model, Config.embeddings.vector_dim)
+        return VoyageAIEmbedder(config.embeddings.model, config.embeddings.vector_dim)
 
-    if Config.embeddings.provider == "openai":
+    if config.embeddings.provider == "openai":
         from haiku.rag.embeddings.openai import Embedder as OpenAIEmbedder
 
-        return OpenAIEmbedder(Config.embeddings.model, Config.embeddings.vector_dim)
+        return OpenAIEmbedder(config.embeddings.model, config.embeddings.vector_dim)
 
-    if Config.embeddings.provider == "vllm":
+    if config.embeddings.provider == "vllm":
         from haiku.rag.embeddings.vllm import Embedder as VllmEmbedder
 
-        return VllmEmbedder(Config.embeddings.model, Config.embeddings.vector_dim)
+        return VllmEmbedder(config.embeddings.model, config.embeddings.vector_dim)
 
-    raise ValueError(f"Unsupported embedding provider: {Config.embeddings.provider}")
+    raise ValueError(f"Unsupported embedding provider: {config.embeddings.provider}")
diff --git a/src/haiku/rag/qa/__init__.py b/src/haiku/rag/qa/__init__.py
index 91adf8f5..4e8e7f92 100644
--- a/src/haiku/rag/qa/__init__.py
+++ b/src/haiku/rag/qa/__init__.py
@@ -1,15 +1,28 @@
 from haiku.rag.client import HaikuRAG
-from haiku.rag.config import Config
+from haiku.rag.config import AppConfig, Config
 from haiku.rag.qa.agent import QuestionAnswerAgent
 
 
 def get_qa_agent(
     client: HaikuRAG,
+    config: AppConfig = Config,
     use_citations: bool = False,
     system_prompt: str | None = None,
 ) -> QuestionAnswerAgent:
-    provider = Config.qa.provider
-    model_name = Config.qa.model
+    """
+    Factory function to get a QA agent based on the configuration.
+
+    Args:
+        client: HaikuRAG client instance.
+        config: Configuration to use. Defaults to global Config.
+        use_citations: Whether to include citations in responses.
+        system_prompt: Optional custom system prompt.
+
+    Returns:
+        A configured QuestionAnswerAgent instance.
+    """
+    provider = config.qa.provider
+    model_name = config.qa.model
 
     return QuestionAnswerAgent(
         client=client,
diff --git a/src/haiku/rag/reranking/__init__.py b/src/haiku/rag/reranking/__init__.py
index 09635430..797aa0f7 100644
--- a/src/haiku/rag/reranking/__init__.py
+++ b/src/haiku/rag/reranking/__init__.py
@@ -1,37 +1,45 @@
 import os
 
-from haiku.rag.config import Config
+from haiku.rag.config import AppConfig, Config
 from haiku.rag.reranking.base import RerankerBase
 
-_reranker: RerankerBase | None = None
+_reranker_cache: dict[int, RerankerBase | None] = {}
 
 
-def get_reranker() -> RerankerBase | None:
+def get_reranker(config: AppConfig = Config) -> RerankerBase | None:
     """
     Factory function to get the appropriate reranker based on the configuration.
-    Returns None if if reranking is disabled.
-    """
-    global _reranker
-    if _reranker is not None:
-        return _reranker
+    Returns None if reranking is disabled.
 
-    if Config.reranking.provider == "mxbai":
+    Args:
+        config: Configuration to use. Defaults to global Config.
+
+    Returns:
+        A reranker instance if configured, None otherwise.
+    """
+    # Use config id as cache key to support multiple configs
+    config_id = id(config)
+    if config_id in _reranker_cache:
+        return _reranker_cache[config_id]
+
+    reranker: RerankerBase | None = None
+
+    if config.reranking.provider == "mxbai":
         try:
             from haiku.rag.reranking.mxbai import MxBAIReranker
 
             os.environ["TOKENIZERS_PARALLELISM"] = "true"
-            _reranker = MxBAIReranker()
-            return _reranker
+            reranker = MxBAIReranker()
         except ImportError:
-            return None
+            reranker = None
 
-    if Config.reranking.provider == "cohere":
+    elif config.reranking.provider == "cohere":
         try:
             from haiku.rag.reranking.cohere import CohereReranker
 
-            _reranker = CohereReranker()
-            return _reranker
+            reranker = CohereReranker()
         except ImportError:
-            return None
+            reranker = None
 
-    return None
+    _reranker_cache[config_id] = reranker
+    return reranker
diff --git a/src/haiku/rag/store/engine.py b/src/haiku/rag/store/engine.py
index e3d56e17..6cbe328e 100644
--- a/src/haiku/rag/store/engine.py
+++ b/src/haiku/rag/store/engine.py
@@ -10,7 +10,7 @@ import lancedb
 from lancedb.pydantic import LanceModel, Vector
 from pydantic import Field
 
-from haiku.rag.config import Config
+from haiku.rag.config import AppConfig, Config
 from haiku.rag.embeddings import get_embedder
 
 logger = logging.getLogger(__name__)
@@ -49,9 +49,12 @@ class SettingsRecord(LanceModel):
 
 
 class Store:
-    def __init__(self, db_path: Path, skip_validation: bool = False):
+    def __init__(
+        self, db_path: Path, config: AppConfig = Config, skip_validation: bool = False
+    ):
         self.db_path: Path = db_path
-        self.embedder = get_embedder()
+        self._config = config
+        self.embedder = get_embedder(config=self._config)
         self._vacuum_lock = asyncio.Lock()
 
         # Create the ChunkRecord model with the correct vector dimension
@@ -59,7 +62,7 @@ class Store:
 
         # Local filesystem handling for DB directory
         if not self._has_cloud_config():
-            if Config.storage.disable_autocreate:
+            if self._config.storage.disable_autocreate:
                 # LanceDB uses a directory path for local databases; enforce presence
                 if not db_path.exists():
                     raise FileNotFoundError(
@@ -85,13 +88,15 @@ class Store:
 
         Args:
             retention_seconds: Retention threshold in seconds. Only versions older
-                              than this will be removed. If None, uses Config.storage.vacuum_retention_seconds.
+                              than this will be removed. If None, uses config.storage.vacuum_retention_seconds.
 
         Note:
             If vacuum is already running, this method returns immediately without blocking.
             Use asyncio.create_task(store.vacuum()) for non-blocking background execution.
         """
-        if self._has_cloud_config() and str(Config.lancedb.uri).startswith("db://"):
+        if self._has_cloud_config() and str(self._config.lancedb.uri).startswith(
+            "db://"
+        ):
             return
 
         # Skip if already running (non-blocking)
@@ -102,7 +107,7 @@ class Store:
             try:
                 # Evaluate config at runtime to allow dynamic changes
                 if retention_seconds is None:
-                    retention_seconds = Config.storage.vacuum_retention_seconds
+                    retention_seconds = self._config.storage.vacuum_retention_seconds
                 # Perform maintenance per table using optimize() with configurable retention
                 retention = timedelta(seconds=retention_seconds)
                 for table in [
@@ -120,9 +125,9 @@ class Store:
         # Check if we have cloud configuration
         if self._has_cloud_config():
             return lancedb.connect(
-                uri=Config.lancedb.uri,
-                api_key=Config.lancedb.api_key,
-                region=Config.lancedb.region,
+                uri=self._config.lancedb.uri,
+                api_key=self._config.lancedb.api_key,
+                region=self._config.lancedb.region,
             )
         else:
             # Local file system connection
@@ -131,7 +136,9 @@ class Store:
     def _has_cloud_config(self) -> bool:
         """Check if cloud configuration is complete."""
         return bool(
-            Config.lancedb.uri and Config.lancedb.api_key and Config.lancedb.region
+            self._config.lancedb.uri
+            and self._config.lancedb.api_key
+            and self._config.lancedb.region
         )
 
     def _validate_configuration(self) -> None:
@@ -173,7 +180,7 @@ class Store:
                 "settings", schema=SettingsRecord
             )
             # Save current settings to the new database
-            settings_data = Config.model_dump(mode="json")
+            settings_data = self._config.model_dump(mode="json")
             self.settings_table.add(
                 [SettingsRecord(id="settings", settings=json.dumps(settings_data))]
             )
diff --git a/src/haiku/rag/store/repositories/chunk.py b/src/haiku/rag/store/repositories/chunk.py
index cfe9cbe3..b92c96de 100644
--- a/src/haiku/rag/store/repositories/chunk.py
+++ b/src/haiku/rag/store/repositories/chunk.py
@@ -6,8 +6,6 @@ from uuid import uuid4
 
 from lancedb.rerankers import RRFReranker
 
-from haiku.rag.config import Config
-from haiku.rag.embeddings import get_embedder
 from haiku.rag.store.engine import DocumentRecord, Store
 from haiku.rag.store.models.chunk import Chunk
 from haiku.rag.utils import load_callable
@@ -23,7 +21,7 @@ class ChunkRepository:
 
     def __init__(self, store: Store) -> None:
         self.store = store
-        self.embedder = get_embedder()
+        self.embedder = store.embedder
 
     def _ensure_fts_index(self) -> None:
         """Ensure FTS index exists on the content column."""
@@ -153,7 +151,7 @@ class ChunkRepository:
 
         # Optionally preprocess markdown before chunking
         processed_document = document
-        preprocessor_path = Config.processing.markdown_preprocessor
+        preprocessor_path = self.store._config.processing.markdown_preprocessor
         if preprocessor_path:
             try:
                 pre_fn = load_callable(preprocessor_path)
diff --git a/src/haiku/rag/store/repositories/settings.py b/src/haiku/rag/store/repositories/settings.py
index e23a7122..4d5bba43 100644
--- a/src/haiku/rag/store/repositories/settings.py
+++ b/src/haiku/rag/store/repositories/settings.py
@@ -1,6 +1,5 @@
 import json
 
-from haiku.rag.config import Config
 from haiku.rag.store.engine import SettingsRecord, Store
 
 
@@ -73,7 +72,7 @@ class SettingsRepository:
 
     def save_current_settings(self) -> None:
         """Save the current configuration to the database."""
-        current_config = Config.model_dump(mode="json")
+        current_config = self.store._config.model_dump(mode="json")
 
         # Check if settings exist
         existing = list(
@@ -116,7 +115,7 @@ class SettingsRepository:
             self.save_current_settings()
             return
 
-        current_config = Config.model_dump(mode="json")
+        current_config = self.store._config.model_dump(mode="json")
 
         # Check if embedding provider or model has changed
         # Support both old flat structure and new nested structure for backward compatibility