diff --git a/src/khoj/processor/markdown/markdown_to_jsonl.py b/src/khoj/processor/markdown/markdown_to_jsonl.py
index 9e08ae89..20cf9b2c 100644
--- a/src/khoj/processor/markdown/markdown_to_jsonl.py
+++ b/src/khoj/processor/markdown/markdown_to_jsonl.py
@@ -129,8 +129,9 @@ class MarkdownToJsonl(TextToJsonl):
         for parsed_entry in parsed_entries:
             entry_filename = Path(entry_to_file_map[parsed_entry])
             # Append base filename to compiled entry for context to model
-            compiled_entry = f"{parsed_entry}\n{entry_filename.stem}"
-            entries.append(Entry(compiled=compiled_entry, raw=parsed_entry, file=f"{entry_filename}"))
+            # Increment heading level for heading entries and make filename as its top level heading
+            prefix = f"# {entry_filename.stem}\n#" if heading else f"# {entry_filename.stem}\n"
+            compiled_entry = f"{prefix}{parsed_entry}"
 
         logger.debug(f"Converted {len(parsed_entries)} markdown entries to dictionaries")
 
diff --git a/tests/test_markdown_to_jsonl.py b/tests/test_markdown_to_jsonl.py
index ca22f359..87a1a07e 100644
--- a/tests/test_markdown_to_jsonl.py
+++ b/tests/test_markdown_to_jsonl.py
@@ -14,6 +14,7 @@ def test_markdown_file_with_no_headings_to_jsonl(tmp_path):
     - Bullet point 2
     """
     markdownfile = create_file(tmp_path, entry)
+    expected_heading = "# " + markdownfile.stem
 
     # Act
     # Extract Entries from specified Markdown files
@@ -27,8 +28,10 @@ def test_markdown_file_with_no_headings_to_jsonl(tmp_path):
 
     # Assert
     assert len(jsonl_data) == 1
-    # Ensure entries with no headings do not get heading prefix prepended
-    assert not jsonl_data[0]["compiled"].startswith("#") and not jsonl_data[0]["raw"].startswith("#")
+    # Ensure raw entry with no headings do not get heading prefix prepended
+    assert not jsonl_data[0]["raw"].startswith("#")
+    # Ensure compiled entry has filename prepended as top level heading
+    assert jsonl_data[0]["compiled"].startswith(expected_heading)
 
 
 def test_single_markdown_entry_to_jsonl(tmp_path):
@@ -130,7 +133,7 @@ def test_extract_entries_with_different_level_headings(tmp_path):
 
 
 # Helper Functions
-def create_file(tmp_path, entry=None, filename="test.md"):
+def create_file(tmp_path: Path, entry=None, filename="test.md"):
     markdown_file = tmp_path / filename
     markdown_file.touch()
     if entry: