diff --git a/cmd/litestream/replicate.go b/cmd/litestream/replicate.go
index 7f9a9aa..fa84907 100644
--- a/cmd/litestream/replicate.go
+++ b/cmd/litestream/replicate.go
@@ -181,7 +181,7 @@ func (c *ReplicateCommand) Run(ctx context.Context) (err error) {
 // Close closes all open databases.
 func (c *ReplicateCommand) Close() (err error) {
 	for _, db := range c.DBs {
-		if e := db.SoftClose(); e != nil {
+		if e := db.Close(); e != nil {
 			log.Printf("error closing db: path=%s err=%s", db.Path(), e)
 			if err == nil {
 				err = e
diff --git a/db.go b/db.go
index ed5a97f..49fbf21 100644
--- a/db.go
+++ b/db.go
@@ -405,20 +405,9 @@ func (db *DB) Open() (err error) {
 	return nil
 }
 
-// Close releases the read lock & closes the database. This method should only
-// be called by tests as it causes the underlying database to be checkpointed.
+// Close flushes outstanding WAL writes to replicas, releases the read lock,
+// and closes the database.
 func (db *DB) Close() (err error) {
-	return db.close(false)
-}
-
-// SoftClose closes everything but the underlying db connection. This method
-// is available because the binary needs to avoid closing the database on exit
-// to prevent autocheckpointing.
-func (db *DB) SoftClose() (err error) {
-	return db.close(true)
-}
-
-func (db *DB) close(soft bool) (err error) {
 	db.cancel()
 	db.wg.Wait()
 
@@ -439,7 +428,7 @@ func (db *DB) close(soft bool) (err error) {
 				err = e
 			}
 		}
-		r.Stop(!soft)
+		r.Stop(true)
 	}
 
 	// Release the read lock to allow other applications to handle checkpointing.
@@ -449,9 +438,7 @@ func (db *DB) close(soft bool) (err error) {
 		}
 	}
 
-	// Only perform full close if this is not a soft close.
-	// This closes the underlying database connection which can clean up the WAL.
-	if !soft && db.db != nil {
+	if db.db != nil {
 		if e := db.db.Close(); e != nil && err == nil {
 			err = e
 		}
@@ -507,8 +494,9 @@ func (db *DB) init() (err error) {
 	dsn := db.path
 	dsn += fmt.Sprintf("?_busy_timeout=%d", BusyTimeout.Milliseconds())
 
-	// Connect to SQLite database.
-	if db.db, err = sql.Open("sqlite3", dsn); err != nil {
+	// Connect to SQLite database. Use the driver registered with a hook to
+	// prevent WAL files from being removed.
+	if db.db, err = sql.Open("litestream-sqlite3", dsn); err != nil {
 		return err
 	}
 
@@ -1536,7 +1524,7 @@ func ApplyWAL(ctx context.Context, dbPath, walPath string) error {
 	}
 
 	// Open SQLite database and force a truncating checkpoint.
-	d, err := sql.Open("sqlite3", dbPath)
+	d, err := sql.Open("litestream-sqlite3", dbPath)
 	if err != nil {
 		return err
 	}
diff --git a/db_test.go b/db_test.go
index fe74225..a9dbb58 100644
--- a/db_test.go
+++ b/db_test.go
@@ -254,8 +254,8 @@ func TestDB_Sync(t *testing.T) {
 			t.Fatal(err)
 		}
 
-		// Verify WAL does not exist.
-		if _, err := os.Stat(db.WALPath()); !os.IsNotExist(err) {
+		// Remove WAL file.
+		if err := os.Remove(db.WALPath()); err != nil {
 			t.Fatal(err)
 		}
 
diff --git a/go.mod b/go.mod
index 286a1d0..169ea19 100644
--- a/go.mod
+++ b/go.mod
@@ -8,7 +8,7 @@ require (
 	github.com/Azure/azure-storage-blob-go v0.14.0
 	github.com/aws/aws-sdk-go v1.42.40
 	github.com/mattn/go-shellwords v1.0.12
-	github.com/mattn/go-sqlite3 v1.14.10
+	github.com/mattn/go-sqlite3 v1.14.11
 	github.com/pierrec/lz4/v4 v4.1.12
 	github.com/pkg/sftp v1.13.4
 	github.com/prometheus/client_golang v1.12.0
diff --git a/go.sum b/go.sum
index ef3f492..7c57594 100644
--- a/go.sum
+++ b/go.sum
@@ -236,6 +236,8 @@ github.com/mattn/go-shellwords v1.0.12 h1:M2zGm7EW6UQJvDeQxo4T51eKPurbeFbe8WtebG
 github.com/mattn/go-shellwords v1.0.12/go.mod h1:EZzvwXDESEeg03EKmM+RmDnNOPKG4lLtQsUlTZDWQ8Y=
 github.com/mattn/go-sqlite3 v1.14.10 h1:MLn+5bFRlWMGoSRmJour3CL1w/qL96mvipqpwQW/Sfk=
 github.com/mattn/go-sqlite3 v1.14.10/go.mod h1:NyWgC/yNuGj7Q9rpYnZvas74GogHl5/Z4A/KQRfk6bU=
+github.com/mattn/go-sqlite3 v1.14.11 h1:gt+cp9c0XGqe9S/wAHTL3n/7MqY+siPWgWJgqdsFrzQ=
+github.com/mattn/go-sqlite3 v1.14.11/go.mod h1:NyWgC/yNuGj7Q9rpYnZvas74GogHl5/Z4A/KQRfk6bU=
 github.com/matttproud/golang_protobuf_extensions v1.0.1 h1:4hp9jkHxhMHkqkrB3Ix0jegS5sx/RkqARlsWZ6pIwiU=
 github.com/matttproud/golang_protobuf_extensions v1.0.1/go.mod h1:D8He9yQNgCq6Z5Ld7szi9bcBfOoFv/3dc6xSMkL2PC0=
 github.com/modern-go/concurrent v0.0.0-20180228061459-e0a39a4cb421/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
diff --git a/litestream.go b/litestream.go
index 98f94a8..5381e05 100644
--- a/litestream.go
+++ b/litestream.go
@@ -13,6 +13,8 @@ import (
 	"strconv"
 	"strings"
 	"time"
+
+	"github.com/mattn/go-sqlite3"
 )
 
 // Naming constants.
@@ -51,6 +53,17 @@ var (
 	LogFlags = 0
 )
 
+func init() {
+	sql.Register("litestream-sqlite3", &sqlite3.SQLiteDriver{
+		ConnectHook: func(conn *sqlite3.SQLiteConn) error {
+			if err := conn.SetFileControlInt("main", sqlite3.SQLITE_FCNTL_PERSIST_WAL, 1); err != nil {
+				return fmt.Errorf("cannot set file control: %w", err)
+			}
+			return nil
+		},
+	})
+}
+
 // SnapshotIterator represents an iterator over a collection of snapshot metadata.
 type SnapshotIterator interface {
 	io.Closer