diff --git a/stack-graphs/src/storage.rs b/stack-graphs/src/storage.rs
index ee39c457e..62f573d5d 100644
--- a/stack-graphs/src/storage.rs
+++ b/stack-graphs/src/storage.rs
@@ -58,6 +58,12 @@ const SCHEMA: &str = r#"
         ) STRICT;
     "#;
 
+const INDEXES: &str = r#"
+        CREATE INDEX IF NOT EXISTS graph_file_value ON graph(file, value);
+        CREATE INDEX IF NOT EXISTS file_paths_file_local_id_value ON file_paths(file, local_id, value);
+        CREATE INDEX IF NOT EXISTS root_paths_symbol_stack_file_value ON root_paths(symbol_stack, file, value);
+    "#;
+
 const PRAGMAS: &str = r#"
         PRAGMA journal_mode = WAL;
         PRAGMA foreign_keys = false;
@@ -147,6 +153,7 @@ impl SQLiteWriter {
     pub fn open_in_memory() -> Result<Self> {
         let mut conn = Connection::open_in_memory()?;
         Self::init(&mut conn)?;
+        Self::init_indexes(&mut conn)?;
         Ok(Self { conn })
     }
 
@@ -161,6 +168,7 @@ impl SQLiteWriter {
         } else {
             check_version(&conn)?;
         }
+        Self::init_indexes(&mut conn)?;
         Ok(Self { conn })
     }
 
@@ -173,6 +181,13 @@ impl SQLiteWriter {
         Ok(())
     }
 
+    fn init_indexes(conn: &mut Connection) -> Result<()> {
+        let tx = conn.transaction()?;
+        tx.execute_batch(INDEXES)?;
+        tx.commit()?;
+        Ok(())
+    }
+
     /// Clean all data from the database.
     pub fn clean_all(&mut self) -> Result<usize> {
         let tx = self.conn.transaction()?;