diff --git a/crates/pinakes-core/tests/common/mod.rs b/crates/pinakes-core/tests/common/mod.rs
index 49a17ba..be07c26 100644
--- a/crates/pinakes-core/tests/common/mod.rs
+++ b/crates/pinakes-core/tests/common/mod.rs
@@ -97,3 +97,41 @@ pub fn create_test_media_item(path: PathBuf, hash: &str) -> MediaItem {
         links_extracted_at: None,
     }
 }
+
+/// Create a test markdown media item with a given ID
+pub fn make_test_markdown_item(id: MediaId) -> MediaItem {
+    let now = chrono::Utc::now();
+    MediaItem {
+        id,
+        path: format!("/tmp/test_{}.md", id.0).into(),
+        file_name: format!("test_{}.md", id.0),
+        media_type: MediaType::Builtin(BuiltinMediaType::Markdown),
+        content_hash: ContentHash::new(format!("hash_{}", id.0)),
+        file_size: 1024,
+        title: Some("Test Note".to_string()),
+        artist: None,
+        album: None,
+        genre: None,
+        year: None,
+        duration_secs: None,
+        description: Some("Test markdown note".to_string()),
+        thumbnail_path: None,
+        custom_fields: HashMap::new(),
+        file_mtime: None,
+        date_taken: None,
+        latitude: None,
+        longitude: None,
+        camera_make: None,
+        camera_model: None,
+        rating: None,
+        perceptual_hash: None,
+        storage_mode: StorageMode::External,
+        original_filename: None,
+        uploaded_at: None,
+        storage_key: None,
+        created_at: now,
+        updated_at: now,
+        deleted_at: None,
+        links_extracted_at: None,
+    }
+}
diff --git a/crates/pinakes-core/tests/markdown_links_atomicity.rs b/crates/pinakes-core/tests/markdown_links_atomicity.rs
new file mode 100644
index 0000000..289a76c
--- /dev/null
+++ b/crates/pinakes-core/tests/markdown_links_atomicity.rs
@@ -0,0 +1,222 @@
+use pinakes_core::links::extract_links;
+use pinakes_core::model::*;
+use pinakes_core::storage::StorageBackend;
+
+mod common;
+
+/// Create test markdown content with multiple links
+fn create_test_note_content(num_links: usize) -> String {
+    let mut content = String::from("# Test Note\n\n");
+    for i in 0..num_links {
+        content.push_str(&format!("Link {}: [[note_{}]]\n", i, i));
+    }
+    content
+}
+
+#[tokio::test]
+async fn test_save_links_atomicity_success_case() {
+    // Setup: Create in-memory database
+    let storage = common::setup().await;
+
+    // Create a test note
+    let note_id = MediaId::new();
+    let item = common::make_test_markdown_item(note_id);
+    storage.insert_media(&item).await.unwrap();
+
+    // Extract links from test content
+    let content = create_test_note_content(5);
+    let links = extract_links(note_id, &content);
+
+    assert_eq!(links.len(), 5, "Should extract 5 links");
+
+    // Save links (first time - should succeed)
+    storage.save_markdown_links(note_id, &links).await.unwrap();
+
+    // Verify all links were saved
+    let saved_links = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(saved_links.len(), 5, "All 5 links should be saved");
+
+    // Update with new links
+    let new_content = create_test_note_content(3);
+    let new_links = extract_links(note_id, &new_content);
+
+    // Save again (should replace old links)
+    storage
+        .save_markdown_links(note_id, &new_links)
+        .await
+        .unwrap();
+
+    // Verify old links were deleted and new links saved
+    let updated_links = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(
+        updated_links.len(),
+        3,
+        "Should have exactly 3 links after update"
+    );
+}
+
+#[tokio::test]
+async fn test_save_links_atomicity_with_valid_data() {
+    // This test verifies that the transaction commit works correctly
+    // by saving links multiple times and ensuring consistency
+    let storage = common::setup().await;
+    let note_id = MediaId::new();
+    let item = common::make_test_markdown_item(note_id);
+    storage.insert_media(&item).await.unwrap();
+
+    // First batch of links
+    let content1 = "[[note1]] and [[note2]]";
+    let links1 = extract_links(note_id, content1);
+    storage.save_markdown_links(note_id, &links1).await.unwrap();
+
+    let saved1 = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(saved1.len(), 2, "First save: 2 links");
+
+    // Second batch (replace)
+    let content2 = "[[note3]] [[note4]] [[note5]]";
+    let links2 = extract_links(note_id, content2);
+    storage.save_markdown_links(note_id, &links2).await.unwrap();
+
+    let saved2 = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(saved2.len(), 3, "Second save: 3 links (old ones deleted)");
+
+    // Third batch (empty)
+    storage.save_markdown_links(note_id, &[]).await.unwrap();
+
+    let saved3 = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(saved3.len(), 0, "Third save: 0 links (all deleted)");
+
+    // Fourth batch (restore some links)
+    let content4 = "[[final_note]]";
+    let links4 = extract_links(note_id, content4);
+    storage.save_markdown_links(note_id, &links4).await.unwrap();
+
+    let saved4 = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(saved4.len(), 1, "Fourth save: 1 link");
+    assert_eq!(saved4[0].target_path, "final_note", "Correct link target");
+}
+
+#[tokio::test]
+async fn test_save_links_idempotency() {
+    // Verify that saving the same links multiple times is safe
+    let storage = common::setup().await;
+    let note_id = MediaId::new();
+    let item = common::make_test_markdown_item(note_id);
+    storage.insert_media(&item).await.unwrap();
+
+    let content = "[[note_a]] [[note_b]]";
+    let links = extract_links(note_id, content);
+
+    // Save same links 3 times
+    storage.save_markdown_links(note_id, &links).await.unwrap();
+    storage.save_markdown_links(note_id, &links).await.unwrap();
+    storage.save_markdown_links(note_id, &links).await.unwrap();
+
+    // Should still have exactly 2 links (not duplicated)
+    let saved = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(
+        saved.len(),
+        2,
+        "Should have exactly 2 links (no duplicates)"
+    );
+}
+
+#[tokio::test]
+async fn test_save_links_concurrent_updates() {
+    // Test that concurrent updates to different notes don't interfere
+    let storage = common::setup().await;
+
+    // Create two different notes
+    let note1_id = MediaId::new();
+    let note2_id = MediaId::new();
+    let item1 = common::make_test_markdown_item(note1_id);
+    let item2 = common::make_test_markdown_item(note2_id);
+    storage.insert_media(&item1).await.unwrap();
+    storage.insert_media(&item2).await.unwrap();
+
+    // Save links for both notes
+    let links1 = extract_links(note1_id, "[[target1]]");
+    let links2 = extract_links(note2_id, "[[target2]] [[target3]]");
+
+    // Execute both saves. We do so in sequence since we can't test true concurrency easily
+    // ...or so I think. Database tests are annoying.
+    storage
+        .save_markdown_links(note1_id, &links1)
+        .await
+        .unwrap();
+    storage
+        .save_markdown_links(note2_id, &links2)
+        .await
+        .unwrap();
+
+    // Verify both notes have correct links
+    let saved1 = storage.get_outgoing_links(note1_id).await.unwrap();
+    let saved2 = storage.get_outgoing_links(note2_id).await.unwrap();
+
+    assert_eq!(saved1.len(), 1, "Note 1 should have 1 link");
+    assert_eq!(saved2.len(), 2, "Note 2 should have 2 links");
+
+    // Update note 1 - should not affect note 2
+    let new_links1 = extract_links(note1_id, "[[target_new1]] [[target_new2]]");
+    storage
+        .save_markdown_links(note1_id, &new_links1)
+        .await
+        .unwrap();
+
+    // Verify note 1 updated but note 2 unchanged
+    let updated1 = storage.get_outgoing_links(note1_id).await.unwrap();
+    let unchanged2 = storage.get_outgoing_links(note2_id).await.unwrap();
+
+    assert_eq!(updated1.len(), 2, "Note 1 should have 2 links after update");
+    assert_eq!(unchanged2.len(), 2, "Note 2 should still have 2 links");
+}
+
+#[tokio::test]
+async fn test_save_links_with_large_batch() {
+    // Test atomicity with a large number of links
+    let storage = common::setup().await;
+    let note_id = MediaId::new();
+    let item = common::make_test_markdown_item(note_id);
+    storage.insert_media(&item).await.unwrap();
+
+    // Create note with 100 links
+    let content = create_test_note_content(100);
+    let links = extract_links(note_id, &content);
+
+    assert_eq!(links.len(), 100, "Should extract 100 links");
+
+    // Save all 100 links
+    storage.save_markdown_links(note_id, &links).await.unwrap();
+
+    // Verify all saved
+    let saved = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(saved.len(), 100, "All 100 links should be saved atomically");
+
+    // Replace with smaller set
+    let small_content = create_test_note_content(10);
+    let small_links = extract_links(note_id, &small_content);
+    storage
+        .save_markdown_links(note_id, &small_links)
+        .await
+        .unwrap();
+
+    // Verify replacement worked
+    let updated = storage.get_outgoing_links(note_id).await.unwrap();
+    assert_eq!(
+        updated.len(),
+        10,
+        "Should have exactly 10 links after replacement"
+    );
+}
+
+// XXX: Testing actual transaction rollback on error is difficult without
+// mocking the database or injecting failures. The above tests verify that:
+// 1. Normal operation is atomic (delete + insert works correctly)
+// 2. Updates properly replace old links
+// 3. Empty link sets work correctly
+// 4. Large batches are handled atomically
+// 5. Concurrent operations on different notes don't interfere
+//
+// The transaction wrapper ensures that if ANY operation fails during
+// the DELETE + INSERT sequence, the entire operation rolls back,
+// preventing partial states.