diff --git a/crates/pinakes-core/src/storage/postgres.rs b/crates/pinakes-core/src/storage/postgres.rs
index ca7b6ba..ed5633f 100644
--- a/crates/pinakes-core/src/storage/postgres.rs
+++ b/crates/pinakes-core/src/storage/postgres.rs
@@ -6047,7 +6047,7 @@ impl StorageBackend for PostgresBackend {
         media_id: MediaId,
         links: &[crate::model::MarkdownLink],
     ) -> Result<()> {
-        let client = self
+        let mut client = self
             .pool
             .get()
             .await
@@ -6055,40 +6055,49 @@ impl StorageBackend for PostgresBackend {
 
         let media_id_str = media_id.0.to_string();
 
-        // Delete existing links for this source
-        client
-            .execute(
-                "DELETE FROM markdown_links WHERE source_media_id = $1",
-                &[&media_id_str],
-            )
+        // Wrap DELETE + INSERT in transaction to ensure atomicity
+        let tx = client
+            .transaction()
             .await
             .map_err(|e| PinakesError::Database(e.to_string()))?;
 
+        // Delete existing links for this source
+        tx.execute(
+            "DELETE FROM markdown_links WHERE source_media_id = $1",
+            &[&media_id_str],
+        )
+        .await
+        .map_err(|e| PinakesError::Database(e.to_string()))?;
+
         // Insert new links
         for link in links {
             let target_media_id = link.target_media_id.map(|id| id.0.to_string());
-            client
-                .execute(
-                    "INSERT INTO markdown_links (
+            tx.execute(
+                "INSERT INTO markdown_links (
                         id, source_media_id, target_path, target_media_id,
                         link_type, link_text, line_number, context, created_at
                     ) VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9)",
-                    &[
-                        &link.id.to_string(),
-                        &media_id_str,
-                        &link.target_path,
-                        &target_media_id,
-                        &link.link_type.to_string(),
-                        &link.link_text,
-                        &link.line_number,
-                        &link.context,
-                        &link.created_at,
-                    ],
-                )
-                .await
-                .map_err(|e| PinakesError::Database(e.to_string()))?;
+                &[
+                    &link.id.to_string(),
+                    &media_id_str,
+                    &link.target_path,
+                    &target_media_id,
+                    &link.link_type.to_string(),
+                    &link.link_text,
+                    &link.line_number,
+                    &link.context,
+                    &link.created_at,
+                ],
+            )
+            .await
+            .map_err(|e| PinakesError::Database(e.to_string()))?;
         }
 
+        // Commit transaction - if this fails, all changes are rolled back
+        tx.commit()
+            .await
+            .map_err(|e| PinakesError::Database(e.to_string()))?;
+
         Ok(())
     }
 
diff --git a/crates/pinakes-core/src/storage/sqlite.rs b/crates/pinakes-core/src/storage/sqlite.rs
index 63c2239..bfd471b 100644
--- a/crates/pinakes-core/src/storage/sqlite.rs
+++ b/crates/pinakes-core/src/storage/sqlite.rs
@@ -6400,16 +6400,19 @@ impl StorageBackend for SqliteBackend {
         let links: Vec<_> = links.to_vec();
 
         tokio::task::spawn_blocking(move || {
-            let conn = conn.lock().unwrap();
+            let mut conn = conn.lock().unwrap();
+
+            // Wrap DELETE + INSERT in transaction to ensure atomicity
+            let tx = conn.transaction()?;
 
             // Delete existing links for this source
-            conn.execute(
+            tx.execute(
                 "DELETE FROM markdown_links WHERE source_media_id = ?1",
                 [&media_id_str],
             )?;
 
             // Insert new links
-            let mut stmt = conn.prepare(
+            let mut stmt = tx.prepare(
                 "INSERT INTO markdown_links (
                     id, source_media_id, target_path, target_media_id,
                     link_type, link_text, line_number, context, created_at
@@ -6430,6 +6433,10 @@ impl StorageBackend for SqliteBackend {
                 ])?;
             }
 
+            // Commit transaction - if this fails, all changes are rolled back
+            drop(stmt);
+            tx.commit()?;
+
             Ok::<_, rusqlite::Error>(())
         })
         .await