diff --git a/crates/matrix-sdk-sqlite/src/crypto_store.rs b/crates/matrix-sdk-sqlite/src/crypto_store.rs
index 28fecd934..ef24833fb 100644
--- a/crates/matrix-sdk-sqlite/src/crypto_store.rs
+++ b/crates/matrix-sdk-sqlite/src/crypto_store.rs
@@ -125,6 +125,8 @@ impl SqliteCryptoStore {
         debug!("Opened sqlite store with version {}", version);
         run_migrations(&conn, version).await?;
 
+        conn.wal_checkpoint().await;
+
         let store_cipher = match secret {
             Some(s) => Some(Arc::new(conn.get_or_create_store_cipher(s).await?)),
             None => None,
diff --git a/crates/matrix-sdk-sqlite/src/event_cache_store.rs b/crates/matrix-sdk-sqlite/src/event_cache_store.rs
index bad1489a5..73eee0a9e 100644
--- a/crates/matrix-sdk-sqlite/src/event_cache_store.rs
+++ b/crates/matrix-sdk-sqlite/src/event_cache_store.rs
@@ -149,8 +149,11 @@ impl SqliteEventCacheStore {
         let conn = pool.get().await?;
 
         let version = conn.db_version().await?;
+
         run_migrations(&conn, version).await?;
 
+        conn.wal_checkpoint().await;
+
         let store_cipher = match secret {
             Some(s) => Some(Arc::new(conn.get_or_create_store_cipher(s).await?)),
             None => None,
diff --git a/crates/matrix-sdk-sqlite/src/media_store.rs b/crates/matrix-sdk-sqlite/src/media_store.rs
index 9584b0365..ae6c229bd 100644
--- a/crates/matrix-sdk-sqlite/src/media_store.rs
+++ b/crates/matrix-sdk-sqlite/src/media_store.rs
@@ -143,6 +143,8 @@ impl SqliteMediaStore {
         let version = conn.db_version().await?;
         run_migrations(&conn, version).await?;
 
+        conn.wal_checkpoint().await;
+
         let store_cipher = match secret {
             Some(s) => Some(Arc::new(conn.get_or_create_store_cipher(s).await?)),
             None => None,
diff --git a/crates/matrix-sdk-sqlite/src/state_store.rs b/crates/matrix-sdk-sqlite/src/state_store.rs
index 5dbc235b9..a760781d6 100644
--- a/crates/matrix-sdk-sqlite/src/state_store.rs
+++ b/crates/matrix-sdk-sqlite/src/state_store.rs
@@ -160,6 +160,8 @@ impl SqliteStateStore {
         };
         this.run_migrations(version, None).await?;
 
+        this.read().await?.wal_checkpoint().await;
+
         Ok(this)
     }