diff --git a/Makefile b/Makefile
index 0e5d0cf..73b3532 100644
--- a/Makefile
+++ b/Makefile
@@ -34,21 +34,10 @@ logs:
 
 # Vector store reindexing
 reindex:
-	$(COMPOSE) exec $(RAGGR) python -c "\
-		import asyncio; \
-		from blueprints.rag.logic import delete_all_documents, index_documents, index_obsidian_documents; \
-		delete_all_documents(); \
-		asyncio.run(index_documents()); \
-		asyncio.run(index_obsidian_documents()); \
-		print('Reindex complete')"
+	$(COMPOSE) exec $(RAGGR) python -m scripts.manage_vectorstore reindex
 
 reindex-obsidian:
-	$(COMPOSE) exec $(RAGGR) python -c "\
-		import asyncio; \
-		from blueprints.rag.logic import delete_documents_by_metadata, index_obsidian_documents; \
-		delete_documents_by_metadata('source', 'obsidian'); \
-		asyncio.run(index_obsidian_documents()); \
-		print('Obsidian reindex complete')"
+	$(COMPOSE) exec $(RAGGR) python -m scripts.manage_vectorstore reindex-obsidian
 
 # YNAB mirror: delta sync, or full re-download
 ynab-sync:
diff --git a/scripts/manage_vectorstore.py b/scripts/manage_vectorstore.py
index cb41dd7..ad37ab3 100644
--- a/scripts/manage_vectorstore.py
+++ b/scripts/manage_vectorstore.py
@@ -7,8 +7,10 @@ import sys
 
 from blueprints.rag.logic import (
     delete_all_documents,
+    delete_documents_by_metadata,
     get_vector_store_stats,
     index_documents,
+    index_obsidian_documents,
     list_all_documents,
 )
 
@@ -31,11 +33,23 @@ async def index():
 
 
 async def reindex():
-    """Clear and reindex all documents."""
+    """Clear and reindex everything: Paperless documents and the Obsidian vault."""
     print("Clearing existing documents...")
     delete_all_documents()
     print("Cleared")
     await index()
+    await reindex_obsidian(clear=False)
+
+
+async def reindex_obsidian(clear: bool = True):
+    """Re-embed the Obsidian vault, leaving Paperless documents alone."""
+    if clear:
+        print("Clearing Obsidian notes...")
+        delete_documents_by_metadata("source", "obsidian")
+    print("Indexing Obsidian vault...")
+    await index_obsidian_documents()
+    print("Obsidian indexing complete!")
+    stats()
 
 
 def list_docs(limit: int = 10, show_content: bool = False):
@@ -60,7 +74,8 @@ def main():
 Examples:
   %(prog)s stats                    # Show vector store statistics
   %(prog)s index                    # Index new documents from Paperless-NGX
-  %(prog)s reindex                  # Clear and reindex all documents
+  %(prog)s reindex                  # Clear and reindex Paperless + Obsidian
+  %(prog)s reindex-obsidian         # Clear and reindex only Obsidian notes
   %(prog)s list 10                  # List first 10 documents
   %(prog)s list 20 --show-content   # List 20 documents with content preview
         """,
@@ -75,7 +90,12 @@ Examples:
     subparsers.add_parser("index", help="Index documents from Paperless-NGX")
 
     # Reindex command
-    subparsers.add_parser("reindex", help="Clear and reindex all documents")
+    subparsers.add_parser(
+        "reindex", help="Clear and reindex Paperless documents and Obsidian notes"
+    )
+    subparsers.add_parser(
+        "reindex-obsidian", help="Clear and reindex only Obsidian notes"
+    )
 
     # List command
     list_parser = subparsers.add_parser("list", help="List documents in vector store")
@@ -99,6 +119,8 @@ Examples:
             asyncio.run(index())
         elif args.command == "reindex":
             asyncio.run(reindex())
+        elif args.command == "reindex-obsidian":
+            asyncio.run(reindex_obsidian())
         elif args.command == "list":
             list_docs(limit=args.limit, show_content=args.show_content)
     except KeyboardInterrupt:
diff --git a/tests/unit/test_manage_vectorstore.py b/tests/unit/test_manage_vectorstore.py
new file mode 100644
index 0000000..cd9324b
--- /dev/null
+++ b/tests/unit/test_manage_vectorstore.py
@@ -0,0 +1,41 @@
+import sys
+from unittest.mock import AsyncMock, MagicMock
+
+import pytest
+
+from scripts import manage_vectorstore as cli
+
+
+@pytest.fixture
+def calls(monkeypatch):
+    calls = []
+    monkeypatch.setattr(cli, "delete_all_documents", lambda: calls.append("delete_all"))
+    monkeypatch.setattr(
+        cli,
+        "delete_documents_by_metadata",
+        lambda k, v: calls.append(f"delete {k}={v}"),
+    )
+    monkeypatch.setattr(
+        cli, "index_documents", AsyncMock(side_effect=lambda: calls.append("paperless"))
+    )
+    monkeypatch.setattr(
+        cli,
+        "index_obsidian_documents",
+        AsyncMock(side_effect=lambda: calls.append("obsidian")),
+    )
+    monkeypatch.setattr(cli, "stats", MagicMock())
+    return calls
+
+
+@pytest.mark.parametrize(
+    "command, expected",
+    [
+        # A full reindex must not drop Obsidian notes after wiping everything.
+        ("reindex", ["delete_all", "paperless", "obsidian"]),
+        ("reindex-obsidian", ["delete source=obsidian", "obsidian"]),
+    ],
+)
+def test_reindex_commands(calls, monkeypatch, command, expected):
+    monkeypatch.setattr(sys, "argv", ["manage_vectorstore", command])
+    cli.main()
+    assert calls == expected