diff --git a/bottomless/src/replicator.rs b/bottomless/src/replicator.rs
index 7850dd4efc..7aa20200c7 100644
--- a/bottomless/src/replicator.rs
+++ b/bottomless/src/replicator.rs
@@ -1677,28 +1677,10 @@ impl Replicator {
         }
         // drop of injector will cause drop&close of last DB connection which will perform final
         // WAL checkpoint of the DB
+        injector
+            .checkpoint()
+            .map_err(|e| anyhow!("unable to apply WAL after restore procedure: {e}"))?;
         drop(injector);
-
-        let db_path_str = db_path
-            .to_str()
-            .ok_or(anyhow!("failed to convert db path to string"))?;
-        let db_wal_file_path = format!("{}-wal", &db_path_str);
-        let db_wal_index_path = format!("{}-shm", &db_path_str);
-        let has_wal_file = tokio::fs::try_exists(&db_wal_file_path).await?;
-        let has_wal_index = tokio::fs::try_exists(&db_wal_index_path).await?;
-        if has_wal_file || has_wal_index {
-            // restore process was not finished successfully as WAL wasn't transferred completely
-            tracing::error!(
-                "WAL wasn't transferred completely during restoration: db_name={}, generation={}",
-                &self.db_name,
-                &generation
-            );
-            let _ = self
-                .remove_wal_files(&db_path_str)
-                .await
-                .inspect_err(|e| tracing::error!("unable to remove wal files: {}", e));
-            return Err(anyhow!("WAL wasn't transferred completely"));
-        }
         Ok(applied_wal_frame)
     }
 
diff --git a/libsql-replication/src/injector/sqlite_injector/mod.rs b/libsql-replication/src/injector/sqlite_injector/mod.rs
index f6ce2aa89f..25669218fd 100644
--- a/libsql-replication/src/injector/sqlite_injector/mod.rs
+++ b/libsql-replication/src/injector/sqlite_injector/mod.rs
@@ -3,7 +3,7 @@ use std::sync::Arc;
 use std::{collections::VecDeque, path::PathBuf};
 
 use parking_lot::Mutex;
-use rusqlite::OpenFlags;
+use rusqlite::{params, OpenFlags};
 use tokio::task::spawn_blocking;
 
 use crate::frame::{Frame, FrameNo};
@@ -25,6 +25,13 @@ pub struct SqliteInjector {
     pub(in super::super) inner: Arc<Mutex<SqliteInjectorInner>>,
 }
 
+impl SqliteInjector {
+    pub fn checkpoint(&mut self) -> Result<()> {
+        let inner = self.inner.clone();
+        return inner.lock().checkpoint();
+    }
+}
+
 impl Injector for SqliteInjector {
     async fn inject_frame(&mut self, frame: RpcFrame) -> Result<Option<FrameNo>> {
         let inner = self.inner.clone();
@@ -124,6 +131,12 @@ impl SqliteInjectorInner {
         })
     }
 
+    pub fn checkpoint(&mut self) -> Result<()> {
+        let conn = self.connection.lock();
+        let _ = conn.query_row("PRAGMA wal_checkpoint(TRUNCATE)", params![], |_| Ok(()))?;
+        Ok(())
+    }
+
     /// Inject a frame into the log. If this was a commit frame, returns Ok(Some(FrameNo)).
     pub fn inject_frame(&mut self, frame: Frame) -> Result<Option<FrameNo>, Error> {
         let frame_close_txn = frame.header().size_after.get() != 0;