diff --git a/backend/plugins/sonarqube/e2e/file_metrics_key_length_migration_test.go b/backend/plugins/sonarqube/e2e/file_metrics_key_length_migration_test.go
new file mode 100644
index 00000000000..3fa1204386e
--- /dev/null
+++ b/backend/plugins/sonarqube/e2e/file_metrics_key_length_migration_test.go
@@ -0,0 +1,109 @@
+/*
+Licensed to the Apache Software Foundation (ASF) under one or more
+contributor license agreements.  See the NOTICE file distributed with
+this work for additional information regarding copyright ownership.
+The ASF licenses this file to You under the Apache License, Version 2.0
+(the "License"); you may not use this file except in compliance with
+the License.  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package e2e
+
+import (
+	"testing"
+
+	"github.com/apache/devlake/core/models/common"
+	"github.com/apache/devlake/helpers/e2ehelper"
+	implcontext "github.com/apache/devlake/impls/context"
+	"github.com/apache/devlake/plugins/sonarqube/impl"
+	sonarqubemigrations "github.com/apache/devlake/plugins/sonarqube/models/migrationscripts"
+	"github.com/stretchr/testify/require"
+)
+
+type sonarqubeFileMetricsBeforeKeyLength struct {
+	ConnectionId   uint64 `gorm:"primaryKey"`
+	FileMetricsKey string `gorm:"primaryKey;type:varchar(191)"`
+	ProjectKey     string `gorm:"index"`
+	common.NoPKModel
+}
+
+func (sonarqubeFileMetricsBeforeKeyLength) TableName() string {
+	return "_tool_sonarqube_file_metrics"
+}
+
+// TestSonarqubeFileMetricsKeyLengthMigrationRerun covers the normal run and a
+// re-run after an interrupted attempt that already dropped the primary key.
+func TestSonarqubeFileMetricsKeyLengthMigrationRerun(t *testing.T) {
+	var sonarqube impl.Sonarqube
+	dataflowTester := e2ehelper.NewDataFlowTester(t, "sonarqube", sonarqube)
+	basicRes := implcontext.NewDefaultBasicRes(dataflowTester.Cfg, dataflowTester.Log, dataflowTester.Dal)
+	const name = "modify _tool_sonarqube_file_metrics file_metrics_key from varchar(191) to varchar(500)"
+
+	// normal run: the primary key exists and is re-created
+	prepareFileMetricsBeforeKeyLength(t, dataflowTester)
+	runMigration(t, sonarqubemigrations.All(), name, basicRes)
+	assertFileMetricsMigrated(t, dataflowTester)
+
+	// re-run: an interrupted attempt dropped the primary key before the
+	// migration history was recorded
+	prepareFileMetricsBeforeKeyLength(t, dataflowTester)
+	if dataflowTester.Dal.Dialect() == "mysql" {
+		require.NoError(t, dataflowTester.Dal.Exec("ALTER TABLE _tool_sonarqube_file_metrics DROP PRIMARY KEY"))
+	} else {
+		require.NoError(t, dataflowTester.Dal.Exec("ALTER TABLE _tool_sonarqube_file_metrics DROP CONSTRAINT _tool_sonarqube_file_metrics_pkey"))
+	}
+	require.False(t, hasPrimaryKey(t, dataflowTester))
+	runMigration(t, sonarqubemigrations.All(), name, basicRes)
+	assertFileMetricsMigrated(t, dataflowTester)
+}
+
+func prepareFileMetricsBeforeKeyLength(t *testing.T, dataflowTester *e2ehelper.DataFlowTester) {
+	t.Helper()
+	require.NoError(t, dataflowTester.Db.Migrator().DropTable(&sonarqubeFileMetricsBeforeKeyLength{}))
+	require.NoError(t, dataflowTester.Db.AutoMigrate(&sonarqubeFileMetricsBeforeKeyLength{}))
+	require.NoError(t, dataflowTester.Db.Create(&sonarqubeFileMetricsBeforeKeyLength{
+		ConnectionId:   1,
+		FileMetricsKey: "project:src/main.go",
+		ProjectKey:     "project",
+	}).Error)
+}
+
+func assertFileMetricsMigrated(t *testing.T, dataflowTester *e2ehelper.DataFlowTester) {
+	t.Helper()
+	require.True(t, hasPrimaryKey(t, dataflowTester))
+	columnTypes, err := dataflowTester.Db.Migrator().ColumnTypes(&sonarqubeFileMetricsBeforeKeyLength{})
+	require.NoError(t, err)
+	for _, columnType := range columnTypes {
+		if columnType.Name() == "file_metrics_key" {
+			length, ok := columnType.Length()
+			require.True(t, ok)
+			require.Equal(t, int64(500), length)
+		}
+	}
+	var migrated sonarqubeFileMetricsBeforeKeyLength
+	require.NoError(t, dataflowTester.Db.First(&migrated, "connection_id = ? AND file_metrics_key = ?", 1, "project:src/main.go").Error)
+	require.Equal(t, "project", migrated.ProjectKey)
+}
+
+func hasPrimaryKey(t *testing.T, dataflowTester *e2ehelper.DataFlowTester) bool {
+	t.Helper()
+	schema := "current_schema()"
+	if dataflowTester.Dal.Dialect() == "mysql" {
+		schema = "DATABASE()"
+	}
+	var count int64
+	require.NoError(t, dataflowTester.Db.Raw(
+		"SELECT COUNT(*) FROM information_schema.table_constraints WHERE table_schema = "+schema+
+			" AND table_name = ? AND constraint_type = 'PRIMARY KEY'",
+		"_tool_sonarqube_file_metrics",
+	).Scan(&count).Error)
+	return count > 0
+}
diff --git a/backend/plugins/sonarqube/models/migrationscripts/20230927_modify_file_metrics_key_length.go b/backend/plugins/sonarqube/models/migrationscripts/20230927_modify_file_metrics_key_length.go
index fb85c1a61ed..c2cce1e992e 100644
--- a/backend/plugins/sonarqube/models/migrationscripts/20230927_modify_file_metrics_key_length.go
+++ b/backend/plugins/sonarqube/models/migrationscripts/20230927_modify_file_metrics_key_length.go
@@ -49,12 +49,23 @@ func (script *modifyFileMetricsKeyLength) Up(basicRes context.BasicRes) errors.E
 	if err1 != nil {
 		return errors.Convert(err1)
 	}
+	// Drop the primary key only if it still exists, so the script can be re-run
+	// after an interrupted attempt that already dropped it.
 	if u.Scheme == "mysql" {
-		if err := db.Exec("ALTER TABLE _tool_sonarqube_file_metrics DROP PRIMARY KEY"); err != nil {
+		pkCount, err := db.Count(
+			dal.From("information_schema.table_constraints"),
+			dal.Where("table_schema = DATABASE() AND table_name = ? AND constraint_type = 'PRIMARY KEY'", "_tool_sonarqube_file_metrics"),
+		)
+		if err != nil {
 			return err
 		}
+		if pkCount > 0 {
+			if err := db.Exec("ALTER TABLE _tool_sonarqube_file_metrics DROP PRIMARY KEY"); err != nil {
+				return err
+			}
+		}
 	} else {
-		if err := db.Exec("ALTER TABLE _tool_sonarqube_file_metrics DROP CONSTRAINT _tool_sonarqube_file_metrics_pkey"); err != nil {
+		if err := db.Exec("ALTER TABLE _tool_sonarqube_file_metrics DROP CONSTRAINT IF EXISTS _tool_sonarqube_file_metrics_pkey"); err != nil {
 			return err
 		}
 	}