diff --git a/crates/matrix-sdk-sqlite/src/crypto_store.rs b/crates/matrix-sdk-sqlite/src/crypto_store.rs
index cb543a40a..2498b92ed 100644
--- a/crates/matrix-sdk-sqlite/src/crypto_store.rs
+++ b/crates/matrix-sdk-sqlite/src/crypto_store.rs
@@ -203,21 +203,24 @@ async fn run_migrations(conn: &SqliteAsyncConn, version: u8) -> Result<()> {
         // the error message: "cannot change into wal mode from within a transaction".
         conn.execute_batch("PRAGMA journal_mode = wal;").await?;
         conn.with_transaction(|txn| {
-            txn.execute_batch(include_str!("../migrations/crypto_store/001_init.sql"))
+            txn.execute_batch(include_str!("../migrations/crypto_store/001_init.sql"))?;
+            txn.set_db_version(1)
         })
         .await?;
     }
 
     if version < 2 {
         conn.with_transaction(|txn| {
-            txn.execute_batch(include_str!("../migrations/crypto_store/002_reset_olm_hash.sql"))
+            txn.execute_batch(include_str!("../migrations/crypto_store/002_reset_olm_hash.sql"))?;
+            txn.set_db_version(2)
         })
         .await?;
     }
 
     if version < 3 {
         conn.with_transaction(|txn| {
-            txn.execute_batch(include_str!("../migrations/crypto_store/003_room_settings.sql"))
+            txn.execute_batch(include_str!("../migrations/crypto_store/003_room_settings.sql"))?;
+            txn.set_db_version(3)
         })
         .await?;
     }
@@ -226,14 +229,16 @@ async fn run_migrations(conn: &SqliteAsyncConn, version: u8) -> Result<()> {
         conn.with_transaction(|txn| {
             txn.execute_batch(include_str!(
                 "../migrations/crypto_store/004_drop_outbound_group_sessions.sql"
-            ))
+            ))?;
+            txn.set_db_version(4)
         })
         .await?;
     }
 
     if version < 5 {
         conn.with_transaction(|txn| {
-            txn.execute_batch(include_str!("../migrations/crypto_store/005_withheld_code.sql"))
+            txn.execute_batch(include_str!("../migrations/crypto_store/005_withheld_code.sql"))?;
+            txn.set_db_version(5)
         })
         .await?;
     }
@@ -242,27 +247,28 @@ async fn run_migrations(conn: &SqliteAsyncConn, version: u8) -> Result<()> {
         conn.with_transaction(|txn| {
             txn.execute_batch(include_str!(
                 "../migrations/crypto_store/006_drop_outbound_group_sessions.sql"
-            ))
+            ))?;
+            txn.set_db_version(6)
         })
         .await?;
     }
 
     if version < 7 {
         conn.with_transaction(|txn| {
-            txn.execute_batch(include_str!("../migrations/crypto_store/007_lock_leases.sql"))
+            txn.execute_batch(include_str!("../migrations/crypto_store/007_lock_leases.sql"))?;
+            txn.set_db_version(7)
         })
         .await?;
     }
 
     if version < 8 {
         conn.with_transaction(|txn| {
-            txn.execute_batch(include_str!("../migrations/crypto_store/008_secret_inbox.sql"))
+            txn.execute_batch(include_str!("../migrations/crypto_store/008_secret_inbox.sql"))?;
+            txn.set_db_version(8)
         })
         .await?;
     }
 
-    conn.set_db_version(DATABASE_VERSION).await?;
-
     Ok(())
 }
 
diff --git a/crates/matrix-sdk-sqlite/src/event_cache_store.rs b/crates/matrix-sdk-sqlite/src/event_cache_store.rs
index 36d9b165a..294b4fd85 100644
--- a/crates/matrix-sdk-sqlite/src/event_cache_store.rs
+++ b/crates/matrix-sdk-sqlite/src/event_cache_store.rs
@@ -13,7 +13,7 @@ use tracing::debug;
 
 use crate::{
     error::{Error, Result},
-    utils::{Key, SqliteAsyncConnExt, SqliteKeyValueStoreAsyncConnExt},
+    utils::{Key, SqliteAsyncConnExt, SqliteKeyValueStoreAsyncConnExt, SqliteKeyValueStoreConnExt},
     OpenStoreError,
 };
 
@@ -83,7 +83,12 @@ impl SqliteEventCacheStore {
     /// version
     ///
     /// If `to` is `None`, the current database version will be used.
-    async fn run_migrations(&self, conn: &SqliteAsyncConn, from: u8, to: Option<u8>) -> Result<()> {
+    async fn run_migrations(
+        &self,
+        _conn: &SqliteAsyncConn,
+        from: u8,
+        to: Option<u8>,
+    ) -> Result<()> {
         let to = to.unwrap_or(DATABASE_VERSION);
 
         if from < to {
@@ -94,8 +99,6 @@ impl SqliteEventCacheStore {
 
         // There is no migration currently since it's the first version of the database.
 
-        conn.set_db_version(to).await?;
-
         Ok(())
     }
 
@@ -144,12 +147,11 @@ async fn init(conn: &SqliteAsyncConn) -> Result<()> {
     // the error message: "cannot change into wal mode from within a transaction".
     conn.execute_batch("PRAGMA journal_mode = wal;").await?;
     conn.with_transaction(|txn| {
-        txn.execute_batch(include_str!("../migrations/event_cache_store/001_init.sql"))
+        txn.execute_batch(include_str!("../migrations/event_cache_store/001_init.sql"))?;
+        txn.set_db_version(1)
     })
     .await?;
 
-    conn.set_db_version(1).await?;
-
     Ok(())
 }
 
diff --git a/crates/matrix-sdk-sqlite/src/state_store.rs b/crates/matrix-sdk-sqlite/src/state_store.rs
index cdf16bf69..610974337 100644
--- a/crates/matrix-sdk-sqlite/src/state_store.rs
+++ b/crates/matrix-sdk-sqlite/src/state_store.rs
@@ -41,7 +41,10 @@ use tracing::{debug, warn};
 
 use crate::{
     error::{Error, Result},
-    utils::{repeat_vars, Key, SqliteAsyncConnExt, SqliteKeyValueStoreAsyncConnExt},
+    utils::{
+        repeat_vars, Key, SqliteAsyncConnExt, SqliteKeyValueStoreAsyncConnExt,
+        SqliteKeyValueStoreConnExt,
+    },
     OpenStoreError,
 };
 
@@ -161,6 +164,7 @@ impl SqliteStateStore {
                     "../migrations/state_store/002_b_replace_room_info.sql"
                 ))?;
 
+                txn.set_db_version(2)?;
                 Result::<_, Error>::Ok(())
             })
             .await?;
@@ -211,6 +215,7 @@ impl SqliteStateStore {
                         .execute((data, room_id))?;
                 }
 
+                txn.set_db_version(3)?;
                 Result::<_, Error>::Ok(())
             })
             .await?;
@@ -220,7 +225,7 @@ impl SqliteStateStore {
             conn.with_transaction(move |txn| {
                 // Create new table.
                 txn.execute_batch(include_str!("../migrations/state_store/003_send_queue.sql"))?;
-                Result::<_, Error>::Ok(())
+                txn.set_db_version(4)
             })
             .await?;
         }
@@ -231,7 +236,7 @@ impl SqliteStateStore {
                 txn.execute_batch(include_str!(
                     "../migrations/state_store/004_send_queue_with_roomid_value.sql"
                 ))?;
-                Result::<_, Error>::Ok(())
+                txn.set_db_version(4)
             })
             .await?;
         }
@@ -242,7 +247,7 @@ impl SqliteStateStore {
                 txn.execute_batch(include_str!(
                     "../migrations/state_store/005_send_queue_dependent_events.sql"
                 ))?;
-                Result::<_, Error>::Ok(())
+                txn.set_db_version(6)
             })
             .await?;
         }
@@ -251,13 +256,11 @@ impl SqliteStateStore {
             conn.with_transaction(move |txn| {
                 // Drop media table.
                 txn.execute_batch(include_str!("../migrations/state_store/006_drop_media.sql"))?;
-                Result::<_, Error>::Ok(())
+                txn.set_db_version(7)
             })
             .await?;
         }
 
-        conn.set_db_version(to).await?;
-
         Ok(())
     }
 
@@ -375,13 +378,12 @@ async fn init(conn: &SqliteAsyncConn) -> Result<()> {
     // the error message: "cannot change into wal mode from within a transaction".
     conn.execute_batch("PRAGMA journal_mode = wal;").await?;
     conn.with_transaction(|txn| {
-        txn.execute_batch(include_str!("../migrations/state_store/001_init.sql"))
+        txn.execute_batch(include_str!("../migrations/state_store/001_init.sql"))?;
+        txn.set_db_version(1)?;
+
+        Ok(())
     })
-    .await?;
-
-    conn.set_db_version(1).await?;
-
-    Ok(())
+    .await
 }
 
 trait SqliteConnectionStateStoreExt {
diff --git a/crates/matrix-sdk-sqlite/src/utils.rs b/crates/matrix-sdk-sqlite/src/utils.rs
index 2ae66ba62..1ec9339e7 100644
--- a/crates/matrix-sdk-sqlite/src/utils.rs
+++ b/crates/matrix-sdk-sqlite/src/utils.rs
@@ -256,6 +256,11 @@ impl<'a> SqliteTransactionExt for Transaction<'a> {
 pub(crate) trait SqliteKeyValueStoreConnExt {
     /// Store the given value for the given key.
     fn set_kv(&self, key: &str, value: &[u8]) -> rusqlite::Result<()>;
+
+    /// Set the version of the database.
+    fn set_db_version(&self, version: u8) -> rusqlite::Result<()> {
+        self.set_kv("version", &[version])
+    }
 }
 
 impl SqliteKeyValueStoreConnExt for rusqlite::Connection {
@@ -317,11 +322,6 @@ pub(crate) trait SqliteKeyValueStoreAsyncConnExt: SqliteAsyncConnExt {
         }
     }
 
-    /// Set the version of the database.
-    async fn set_db_version(&self, version: u8) -> rusqlite::Result<()> {
-        self.set_kv("version", vec![version]).await
-    }
-
     /// Get the [`StoreCipher`] of the database or create it.
     async fn get_or_create_store_cipher(
         &self,