diff --git a/backend/open_webui/config.py b/backend/open_webui/config.py
index 2f052ca6e..08a30815b 100644
--- a/backend/open_webui/config.py
+++ b/backend/open_webui/config.py
@@ -2862,6 +2862,12 @@ RAG_TEXT_SPLITTER = PersistentConfig(
     os.environ.get("RAG_TEXT_SPLITTER", ""),
 )
 
+ENABLE_MARKDOWN_HEADER_TEXT_SPLITTER = PersistentConfig(
+    "ENABLE_MARKDOWN_HEADER_TEXT_SPLITTER",
+    "rag.enable_markdown_header_text_splitter",
+    os.environ.get("ENABLE_MARKDOWN_HEADER_TEXT_SPLITTER", "True").lower() == "true",
+)
+
 
 TIKTOKEN_CACHE_DIR = os.environ.get("TIKTOKEN_CACHE_DIR", f"{CACHE_DIR}/tiktoken")
 TIKTOKEN_ENCODING_NAME = PersistentConfig(
diff --git a/backend/open_webui/main.py b/backend/open_webui/main.py
index 7e5a19498..68c90c7ee 100644
--- a/backend/open_webui/main.py
+++ b/backend/open_webui/main.py
@@ -282,6 +282,7 @@ from open_webui.config import (
     MISTRAL_OCR_API_BASE_URL,
     MISTRAL_OCR_API_KEY,
     RAG_TEXT_SPLITTER,
+    ENABLE_MARKDOWN_HEADER_TEXT_SPLITTER,
     TIKTOKEN_ENCODING_NAME,
     PDF_EXTRACT_IMAGES,
     YOUTUBE_LOADER_LANGUAGE,
@@ -888,6 +889,10 @@ app.state.config.MINERU_API_TIMEOUT = MINERU_API_TIMEOUT
 app.state.config.MINERU_PARAMS = MINERU_PARAMS
 
 app.state.config.TEXT_SPLITTER = RAG_TEXT_SPLITTER
+app.state.config.ENABLE_MARKDOWN_HEADER_TEXT_SPLITTER = (
+    ENABLE_MARKDOWN_HEADER_TEXT_SPLITTER
+)
+
 app.state.config.TIKTOKEN_ENCODING_NAME = TIKTOKEN_ENCODING_NAME
 
 app.state.config.CHUNK_SIZE = CHUNK_SIZE
diff --git a/backend/open_webui/routers/retrieval.py b/backend/open_webui/routers/retrieval.py
index c24ebf8d5..6f6b97fb9 100644
--- a/backend/open_webui/routers/retrieval.py
+++ b/backend/open_webui/routers/retrieval.py
@@ -1312,6 +1312,27 @@ def save_docs_to_vector_db(
                 raise ValueError(ERROR_MESSAGES.DUPLICATE_CONTENT)
 
     if split:
+        if request.app.state.config.ENABLE_MARKDOWN_HEADER_TEXT_SPLITTER:
+            log.info("Using markdown header text splitter")
+
+            # Define headers to split on - covering most common markdown header levels
+            markdown_splitter = MarkdownHeaderTextSplitter(
+                headers_to_split_on=[
+                    ("#", "Header 1"),
+                    ("##", "Header 2"),
+                    ("###", "Header 3"),
+                    ("####", "Header 4"),
+                    ("#####", "Header 5"),
+                    ("######", "Header 6"),
+                ],
+                strip_headers=False,  # Keep headers in content for context
+            )
+
+            split_docs = []
+            for doc in docs:
+                split_docs.extend(markdown_splitter.split_text(doc.page_content))
+            docs = split_docs
+
         if request.app.state.config.TEXT_SPLITTER in ["", "character"]:
             text_splitter = RecursiveCharacterTextSplitter(
                 chunk_size=request.app.state.config.CHUNK_SIZE,
@@ -1332,52 +1353,6 @@ def save_docs_to_vector_db(
                 add_start_index=True,
             )
             docs = text_splitter.split_documents(docs)
-        elif request.app.state.config.TEXT_SPLITTER == "markdown_header":
-            log.info("Using markdown header text splitter")
-
-            # Define headers to split on - covering most common markdown header levels
-            headers_to_split_on = [
-                ("#", "Header 1"),
-                ("##", "Header 2"),
-                ("###", "Header 3"),
-                ("####", "Header 4"),
-                ("#####", "Header 5"),
-                ("######", "Header 6"),
-            ]
-
-            markdown_splitter = MarkdownHeaderTextSplitter(
-                headers_to_split_on=headers_to_split_on,
-                strip_headers=False,  # Keep headers in content for context
-            )
-
-            md_split_docs = []
-            for doc in docs:
-                md_header_splits = markdown_splitter.split_text(doc.page_content)
-                text_splitter = RecursiveCharacterTextSplitter(
-                    chunk_size=request.app.state.config.CHUNK_SIZE,
-                    chunk_overlap=request.app.state.config.CHUNK_OVERLAP,
-                    add_start_index=True,
-                )
-                md_header_splits = text_splitter.split_documents(md_header_splits)
-
-                # Convert back to Document objects, preserving original metadata
-                for split_chunk in md_header_splits:
-                    headings_list = []
-                    # Extract header values in order based on headers_to_split_on
-                    for _, header_meta_key_name in headers_to_split_on:
-                        if header_meta_key_name in split_chunk.metadata:
-                            headings_list.append(
-                                split_chunk.metadata[header_meta_key_name]
-                            )
-
-                    md_split_docs.append(
-                        Document(
-                            page_content=split_chunk.page_content,
-                            metadata={**doc.metadata, "headings": headings_list},
-                        )
-                    )
-
-            docs = md_split_docs
         else:
             raise ValueError(ERROR_MESSAGES.DEFAULT("Invalid text splitter"))
 
@@ -2424,7 +2399,11 @@ class DeleteForm(BaseModel):
 
 
 @router.post("/delete")
-def delete_entries_from_collection(form_data: DeleteForm, user=Depends(get_admin_user), db: Session = Depends(get_session)):
+def delete_entries_from_collection(
+    form_data: DeleteForm,
+    user=Depends(get_admin_user),
+    db: Session = Depends(get_session),
+):
     try:
         if VECTOR_DB_CLIENT.has_collection(collection_name=form_data.collection_name):
             file = Files.get_file_by_id(form_data.file_id, db=db)
@@ -2566,7 +2545,9 @@ async def process_files_batch(
 
             # Update all files with collection name
             for file_update, file_result in zip(file_updates, file_results):
-                Files.update_file_by_id(id=file_result.file_id, form_data=file_update, db=db)
+                Files.update_file_by_id(
+                    id=file_result.file_id, form_data=file_update, db=db
+                )
                 file_result.status = "completed"
 
         except Exception as e: