diff --git a/integration/alertmanager_test.go b/integration/alertmanager_test.go
index 0d6313b808e..e1790f005a2 100644
--- a/integration/alertmanager_test.go
+++ b/integration/alertmanager_test.go
@@ -25,8 +25,8 @@ func TestAlertmanager(t *testing.T) {
 	alertmanager := e2ecortex.NewAlertmanager(
 		"alertmanager",
 		mergeFlags(
-			AlertmanagerFlags,
-			AlertmanagerLocalFlags,
+			AlertmanagerFlags(),
+			AlertmanagerLocalFlags(),
 		),
 		"",
 	)
@@ -56,15 +56,14 @@ func TestAlertmanagerStoreAPI(t *testing.T) {
 	require.NoError(t, err)
 	defer s.Close()
 
-	minio := e2edb.NewMinio(9000, AlertmanagerS3Flags["-alertmanager.storage.s3.buckets"])
+	flags := mergeFlags(AlertmanagerFlags(), AlertmanagerS3Flags())
+
+	minio := e2edb.NewMinio(9000, flags["-alertmanager.storage.s3.buckets"])
 	require.NoError(t, s.StartAndWaitReady(minio))
 
 	am := e2ecortex.NewAlertmanager(
 		"alertmanager",
-		mergeFlags(
-			AlertmanagerFlags,
-			AlertmanagerS3Flags,
-		),
+		flags,
 		"",
 	)
 
diff --git a/integration/backward_compatibility_test.go b/integration/backward_compatibility_test.go
index 6c56589282e..52502d302d1 100644
--- a/integration/backward_compatibility_test.go
+++ b/integration/backward_compatibility_test.go
@@ -41,7 +41,7 @@ func preCortex14Flags(flags map[string]string) map[string]string {
 func TestBackwardCompatibilityWithChunksStorage(t *testing.T) {
 	for previousImage, flagsFn := range previousVersionImages {
 		t.Run(fmt.Sprintf("Backward compatibility upgrading from %s", previousImage), func(t *testing.T) {
-			flags := ChunksStorageFlags
+			flags := ChunksStorageFlags()
 			if flagsFn != nil {
 				flags = flagsFn(flags)
 			}
@@ -54,7 +54,7 @@ func TestBackwardCompatibilityWithChunksStorage(t *testing.T) {
 func TestNewDistributorsCanPushToOldIngestersWithReplication(t *testing.T) {
 	for previousImage, flagsFn := range previousVersionImages {
 		t.Run(fmt.Sprintf("Backward compatibility upgrading from %s", previousImage), func(t *testing.T) {
-			flags := ChunksStorageFlags
+			flags := ChunksStorageFlags()
 			if flagsFn != nil {
 				flags = flagsFn(flags)
 			}
@@ -78,7 +78,7 @@ func runBackwardCompatibilityTestWithChunksStorage(t *testing.T, previousImage s
 
 	// Start Cortex table-manager (running on current version since the backward compatibility
 	// test is about testing a rolling update of other services).
-	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
+	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags(), "")
 	require.NoError(t, s.StartAndWaitReady(tableManager))
 
 	// Wait until the first table-manager sync has completed, so that we're
@@ -87,7 +87,7 @@ func runBackwardCompatibilityTestWithChunksStorage(t *testing.T, previousImage s
 
 	// Start other Cortex components (ingester running on previous version).
 	ingester1 := e2ecortex.NewIngester("ingester-1", consul.NetworkHTTPEndpoint(), flagsForOldImage, previousImage)
-	distributor := e2ecortex.NewDistributor("distributor", consul.NetworkHTTPEndpoint(), ChunksStorageFlags, "")
+	distributor := e2ecortex.NewDistributor("distributor", consul.NetworkHTTPEndpoint(), ChunksStorageFlags(), "")
 	require.NoError(t, s.StartAndWaitReady(distributor, ingester1))
 
 	// Wait until the distributor has updated the ring.
@@ -104,7 +104,7 @@ func runBackwardCompatibilityTestWithChunksStorage(t *testing.T, previousImage s
 	require.NoError(t, err)
 	require.Equal(t, 200, res.StatusCode)
 
-	ingester2 := e2ecortex.NewIngester("ingester-2", consul.NetworkHTTPEndpoint(), mergeFlags(ChunksStorageFlags, map[string]string{
+	ingester2 := e2ecortex.NewIngester("ingester-2", consul.NetworkHTTPEndpoint(), mergeFlags(ChunksStorageFlags(), map[string]string{
 		"-ingester.join-after": "10s",
 	}), "")
 	// Start ingester-2 on new version, to ensure the transfer is backward compatible.
@@ -117,7 +117,8 @@ func runBackwardCompatibilityTestWithChunksStorage(t *testing.T, previousImage s
 	checkQueries(t, consul, distributor,
 		expectedVector,
 		previousImage,
-		flagsForOldImage, ChunksStorageFlags,
+		flagsForOldImage,
+		ChunksStorageFlags(),
 		now,
 		s,
 		1,
@@ -135,7 +136,7 @@ func runNewDistributorsCanPushToOldIngestersWithReplication(t *testing.T, previo
 	consul := e2edb.NewConsul()
 	require.NoError(t, s.StartAndWaitReady(dynamo, consul))
 
-	flagsForNewImage := mergeFlags(ChunksStorageFlags, map[string]string{
+	flagsForNewImage := mergeFlags(ChunksStorageFlags(), map[string]string{
 		"-distributor.replication-factor": "3",
 	})
 
@@ -143,7 +144,7 @@ func runNewDistributorsCanPushToOldIngestersWithReplication(t *testing.T, previo
 
 	// Start Cortex table-manager (running on current version since the backward compatibility
 	// test is about testing a rolling update of other services).
-	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
+	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags(), "")
 	require.NoError(t, s.StartAndWaitReady(tableManager))
 
 	// Wait until the first table-manager sync has completed, so that we're
@@ -174,7 +175,8 @@ func runNewDistributorsCanPushToOldIngestersWithReplication(t *testing.T, previo
 	checkQueries(t, consul, distributor,
 		expectedVector,
 		previousImage,
-		flagsForPreviousImage, flagsForNewImage,
+		flagsForPreviousImage,
+		flagsForNewImage,
 		now,
 		s,
 		3,
diff --git a/integration/chunks_delete_series_test.go b/integration/chunks_delete_series_test.go
index 2ed12899979..22e1feff6df 100644
--- a/integration/chunks_delete_series_test.go
+++ b/integration/chunks_delete_series_test.go
@@ -43,7 +43,7 @@ func TestDeleteSeriesAllIndexBackends(t *testing.T) {
 		storeConfigs[i] = storeConfig{From: oldestStoreStartTime.Add(time.Duration(i) * perStoreDuration).UTC().Format("2006-01-02"), IndexStore: store}
 	}
 
-	flags := mergeFlags(ChunksStorageFlags, map[string]string{
+	flags := mergeFlags(ChunksStorageFlags(), map[string]string{
 		"-cassandra.addresses":          cassandra.NetworkHTTPEndpoint(),
 		"-cassandra.keyspace":           "tests", // keyspace gets created on startup if it does not exist
 		"-cassandra.replication-factor": "1",
diff --git a/integration/chunks_storage_backends_test.go b/integration/chunks_storage_backends_test.go
index c92d034550e..45198ae0b69 100644
--- a/integration/chunks_storage_backends_test.go
+++ b/integration/chunks_storage_backends_test.go
@@ -60,7 +60,7 @@ func TestChunksStorageAllIndexBackends(t *testing.T) {
 		storeConfigs[i] = storeConfig{From: oldestStoreStartTime.Add(time.Duration(i) * perStoreDuration).Format("2006-01-02"), IndexStore: store}
 	}
 
-	storageFlags := mergeFlags(ChunksStorageFlags, map[string]string{
+	storageFlags := mergeFlags(ChunksStorageFlags(), map[string]string{
 		"-cassandra.addresses":          cassandra.NetworkHTTPEndpoint(),
 		"-cassandra.keyspace":           "tests", // keyspace gets created on startup if it does not exist
 		"-cassandra.replication-factor": "1",
diff --git a/integration/configs.go b/integration/configs.go
index 64029d535d7..da084871de6 100644
--- a/integration/configs.go
+++ b/integration/configs.go
@@ -90,46 +90,56 @@ receivers:
 var (
 	cortexSchemaConfigYaml = buildSchemaConfigWith([]storeConfig{{From: "2019-03-20", IndexStore: "aws-dynamo"}})
 
-	AlertmanagerFlags = map[string]string{
-		"-alertmanager.configs.poll-interval": "1s",
-		"-alertmanager.web.external-url":      "http://localhost/api/prom",
+	AlertmanagerFlags = func() map[string]string {
+		return map[string]string{
+			"-alertmanager.configs.poll-interval": "1s",
+			"-alertmanager.web.external-url":      "http://localhost/api/prom",
+		}
 	}
 
-	AlertmanagerLocalFlags = map[string]string{
-		"-alertmanager.storage.type":       "local",
-		"-alertmanager.storage.local.path": filepath.Join(e2e.ContainerSharedDir, "alertmanager_configs"),
+	AlertmanagerLocalFlags = func() map[string]string {
+		return map[string]string{
+			"-alertmanager.storage.type":       "local",
+			"-alertmanager.storage.local.path": filepath.Join(e2e.ContainerSharedDir, "alertmanager_configs"),
+		}
 	}
 
-	AlertmanagerS3Flags = map[string]string{
-		"-alertmanager.storage.type":                "s3",
-		"-alertmanager.storage.s3.buckets":          "cortex-alerts",
-		"-alertmanager.storage.s3.force-path-style": "true",
-		"-alertmanager.storage.s3.url":              fmt.Sprintf("s3://%s:%s@%s-minio-9000.:9000", e2edb.MinioAccessKey, e2edb.MinioSecretKey, networkName),
+	AlertmanagerS3Flags = func() map[string]string {
+		return map[string]string{
+			"-alertmanager.storage.type":                "s3",
+			"-alertmanager.storage.s3.buckets":          "cortex-alerts",
+			"-alertmanager.storage.s3.force-path-style": "true",
+			"-alertmanager.storage.s3.url":              fmt.Sprintf("s3://%s:%s@%s-minio-9000.:9000", e2edb.MinioAccessKey, e2edb.MinioSecretKey, networkName),
+		}
 	}
 
-	RulerConfigs = map[string]string{
-		"-ruler.enable-sharding":             "false",
-		"-ruler.poll-interval":               "2s",
-		"-experimental.ruler.enable-api":     "true",
-		"-ruler.storage.type":                "s3",
-		"-ruler.storage.s3.buckets":          "cortex-rules",
-		"-ruler.storage.s3.force-path-style": "true",
-		"-ruler.storage.s3.url":              fmt.Sprintf("s3://%s:%s@%s-minio-9000.:9000", e2edb.MinioAccessKey, e2edb.MinioSecretKey, networkName),
+	RulerFlags = func() map[string]string {
+		return map[string]string{
+			"-ruler.enable-sharding":             "false",
+			"-ruler.poll-interval":               "2s",
+			"-experimental.ruler.enable-api":     "true",
+			"-ruler.storage.type":                "s3",
+			"-ruler.storage.s3.buckets":          "cortex-rules",
+			"-ruler.storage.s3.force-path-style": "true",
+			"-ruler.storage.s3.url":              fmt.Sprintf("s3://%s:%s@%s-minio-9000.:9000", e2edb.MinioAccessKey, e2edb.MinioSecretKey, networkName),
+		}
 	}
 
-	BlocksStorageFlags = map[string]string{
-		"-store.engine":                                 blocksStorageEngine,
-		"-blocks-storage.backend":                       "s3",
-		"-blocks-storage.tsdb.block-ranges-period":      "1m",
-		"-blocks-storage.bucket-store.sync-interval":    "5s",
-		"-blocks-storage.tsdb.retention-period":         "5m",
-		"-blocks-storage.tsdb.ship-interval":            "1m",
-		"-blocks-storage.tsdb.head-compaction-interval": "1s",
-		"-blocks-storage.s3.access-key-id":              e2edb.MinioAccessKey,
-		"-blocks-storage.s3.secret-access-key":          e2edb.MinioSecretKey,
-		"-blocks-storage.s3.bucket-name":                bucketName,
-		"-blocks-storage.s3.endpoint":                   fmt.Sprintf("%s-minio-9000:9000", networkName),
-		"-blocks-storage.s3.insecure":                   "true",
+	BlocksStorageFlags = func() map[string]string {
+		return map[string]string{
+			"-store.engine":                                 blocksStorageEngine,
+			"-blocks-storage.backend":                       "s3",
+			"-blocks-storage.tsdb.block-ranges-period":      "1m",
+			"-blocks-storage.bucket-store.sync-interval":    "5s",
+			"-blocks-storage.tsdb.retention-period":         "5m",
+			"-blocks-storage.tsdb.ship-interval":            "1m",
+			"-blocks-storage.tsdb.head-compaction-interval": "1s",
+			"-blocks-storage.s3.access-key-id":              e2edb.MinioAccessKey,
+			"-blocks-storage.s3.secret-access-key":          e2edb.MinioSecretKey,
+			"-blocks-storage.s3.bucket-name":                bucketName,
+			"-blocks-storage.s3.endpoint":                   fmt.Sprintf("%s-minio-9000:9000", networkName),
+			"-blocks-storage.s3.insecure":                   "true",
+		}
 	}
 
 	BlocksStorageConfig = buildConfigFromTemplate(`
@@ -163,11 +173,13 @@ blocks_storage:
 		MinioEndpoint:  fmt.Sprintf("%s-minio-9000:9000", networkName),
 	})
 
-	ChunksStorageFlags = map[string]string{
-		"-dynamodb.url":                   fmt.Sprintf("dynamodb://u:p@%s-dynamodb.:8000", networkName),
-		"-table-manager.poll-interval":    "1m",
-		"-schema-config-file":             filepath.Join(e2e.ContainerSharedDir, cortexSchemaConfigFile),
-		"-table-manager.retention-period": "168h",
+	ChunksStorageFlags = func() map[string]string {
+		return map[string]string{
+			"-dynamodb.url":                   fmt.Sprintf("dynamodb://u:p@%s-dynamodb.:8000", networkName),
+			"-table-manager.poll-interval":    "1m",
+			"-schema-config-file":             filepath.Join(e2e.ContainerSharedDir, cortexSchemaConfigFile),
+			"-table-manager.retention-period": "168h",
+		}
 	}
 
 	ChunksStorageConfig = buildConfigFromTemplate(`
diff --git a/integration/ingester_flush_test.go b/integration/ingester_flush_test.go
index 5bd3dc7df96..cd713e8656a 100644
--- a/integration/ingester_flush_test.go
+++ b/integration/ingester_flush_test.go
@@ -32,12 +32,12 @@ func TestIngesterFlushWithChunksStorage(t *testing.T) {
 	// Start Cortex components.
 	require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
 
-	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
-	ingester := e2ecortex.NewIngester("ingester", consul.NetworkHTTPEndpoint(), mergeFlags(ChunksStorageFlags, map[string]string{
+	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags(), "")
+	ingester := e2ecortex.NewIngester("ingester", consul.NetworkHTTPEndpoint(), mergeFlags(ChunksStorageFlags(), map[string]string{
 		"-ingester.max-transfer-retries": "0",
 	}), "")
-	querier := e2ecortex.NewQuerier("querier", consul.NetworkHTTPEndpoint(), ChunksStorageFlags, "")
-	distributor := e2ecortex.NewDistributor("distributor", consul.NetworkHTTPEndpoint(), ChunksStorageFlags, "")
+	querier := e2ecortex.NewQuerier("querier", consul.NetworkHTTPEndpoint(), ChunksStorageFlags(), "")
+	distributor := e2ecortex.NewDistributor("distributor", consul.NetworkHTTPEndpoint(), ChunksStorageFlags(), "")
 	require.NoError(t, s.StartAndWaitReady(distributor, querier, ingester, tableManager))
 
 	// Wait until the first table-manager sync has completed, so that we're
diff --git a/integration/ingester_hand_over_test.go b/integration/ingester_hand_over_test.go
index 81255300fa1..8e362eff024 100644
--- a/integration/ingester_hand_over_test.go
+++ b/integration/ingester_hand_over_test.go
@@ -17,13 +17,13 @@ import (
 )
 
 func TestIngesterHandOverWithChunksStorage(t *testing.T) {
-	runIngesterHandOverTest(t, ChunksStorageFlags, func(t *testing.T, s *e2e.Scenario) {
+	runIngesterHandOverTest(t, ChunksStorageFlags(), func(t *testing.T, s *e2e.Scenario) {
 		dynamo := e2edb.NewDynamoDB()
 		require.NoError(t, s.StartAndWaitReady(dynamo))
 
 		require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
 
-		tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
+		tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags(), "")
 		require.NoError(t, s.StartAndWaitReady(tableManager))
 
 		// Wait until the first table-manager sync has completed, so that we're
diff --git a/integration/ingester_sharding_test.go b/integration/ingester_sharding_test.go
index 4b60c5e8f2a..337e78d119b 100644
--- a/integration/ingester_sharding_test.go
+++ b/integration/ingester_sharding_test.go
@@ -44,7 +44,7 @@ func TestIngesterSharding(t *testing.T) {
 			require.NoError(t, err)
 			defer s.Close()
 
-			flags := BlocksStorageFlags
+			flags := BlocksStorageFlags()
 			flags["-distributor.shard-by-all-labels"] = "true"
 			flags["-distributor.sharding-strategy"] = testData.shardingStrategy
 			flags["-distributor.ingestion-tenant-shard-size"] = strconv.Itoa(testData.tenantShardSize)
diff --git a/integration/integration_memberlist_single_binary_test.go b/integration/integration_memberlist_single_binary_test.go
index dcf9f270f43..883db8c0bb6 100644
--- a/integration/integration_memberlist_single_binary_test.go
+++ b/integration/integration_memberlist_single_binary_test.go
@@ -77,7 +77,7 @@ func newSingleBinary(name string, join string) *e2ecortex.CortexService {
 
 	serv := e2ecortex.NewSingleBinary(
 		name,
-		mergeFlags(ChunksStorageFlags, flags),
+		mergeFlags(ChunksStorageFlags(), flags),
 		"",
 		8000,
 	)
diff --git a/integration/querier_remote_read_test.go b/integration/querier_remote_read_test.go
index 5bc0388ebff..ae2b31cef23 100644
--- a/integration/querier_remote_read_test.go
+++ b/integration/querier_remote_read_test.go
@@ -29,7 +29,7 @@ func TestQuerierRemoteRead(t *testing.T) {
 	defer s.Close()
 
 	require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
-	flags := mergeFlags(ChunksStorageFlags, map[string]string{})
+	flags := mergeFlags(ChunksStorageFlags(), map[string]string{})
 
 	// Start dependencies.
 	dynamo := e2edb.NewDynamoDB()
@@ -37,7 +37,7 @@ func TestQuerierRemoteRead(t *testing.T) {
 	consul := e2edb.NewConsul()
 	require.NoError(t, s.StartAndWaitReady(consul, dynamo))
 
-	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
+	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags(), "")
 	require.NoError(t, s.StartAndWaitReady(tableManager))
 
 	// Wait until the first table-manager sync has completed, so that we're
@@ -63,7 +63,7 @@ func TestQuerierRemoteRead(t *testing.T) {
 	require.NoError(t, err)
 	require.Equal(t, 200, res.StatusCode)
 
-	querier := e2ecortex.NewQuerier("querier", consul.NetworkHTTPEndpoint(), ChunksStorageFlags, "")
+	querier := e2ecortex.NewQuerier("querier", consul.NetworkHTTPEndpoint(), ChunksStorageFlags(), "")
 	require.NoError(t, s.StartAndWaitReady(querier))
 
 	// Wait until the querier has updated the ring.
diff --git a/integration/querier_sharding_test.go b/integration/querier_sharding_test.go
index d205b7e16f2..82ead391755 100644
--- a/integration/querier_sharding_test.go
+++ b/integration/querier_sharding_test.go
@@ -39,12 +39,7 @@ func runQuerierShardingTest(t *testing.T, sharding bool) {
 	consul := e2edb.NewConsul()
 	require.NoError(t, s.StartAndWaitReady(consul, memcached))
 
-	minio := e2edb.NewMinio(9000, BlocksStorageFlags["-blocks-storage.s3.bucket-name"])
-	require.NoError(t, s.StartAndWaitReady(minio))
-
-	flags := BlocksStorageFlags
-
-	flags = mergeFlags(flags, map[string]string{
+	flags := mergeFlags(BlocksStorageFlags(), map[string]string{
 		"-querier.cache-results":                       "true",
 		"-querier.split-queries-by-interval":           "24h",
 		"-querier.query-ingesters-within":              "12h", // Required by the test on query /series out of ingesters time range
@@ -52,6 +47,9 @@ func runQuerierShardingTest(t *testing.T, sharding bool) {
 		"-querier.max-outstanding-requests-per-tenant": strconv.Itoa(numQueries), // To avoid getting errors.
 	})
 
+	minio := e2edb.NewMinio(9000, flags["-blocks-storage.s3.bucket-name"])
+	require.NoError(t, s.StartAndWaitReady(minio))
+
 	if sharding {
 		// Use only single querier for each user.
 		flags["-frontend.max-queriers-per-tenant"] = "1"
diff --git a/integration/querier_streaming_mixed_ingester_test.go b/integration/querier_streaming_mixed_ingester_test.go
index 16e3d321658..ee347171c51 100644
--- a/integration/querier_streaming_mixed_ingester_test.go
+++ b/integration/querier_streaming_mixed_ingester_test.go
@@ -26,9 +26,8 @@ func TestQuerierWithStreamingBlocksAndChunksIngesters(t *testing.T) {
 	defer s.Close()
 
 	require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
-	chunksFlags := mergeFlags(ChunksStorageFlags, map[string]string{})
-
-	blockFlags := mergeFlags(BlocksStorageFlags, map[string]string{
+	chunksFlags := ChunksStorageFlags()
+	blockFlags := mergeFlags(BlocksStorageFlags(), map[string]string{
 		"-blocks-storage.tsdb.block-ranges-period":      "1h",
 		"-blocks-storage.tsdb.head-compaction-interval": "1m",
 		"-store-gateway.sharding-enabled":               "false",
diff --git a/integration/querier_test.go b/integration/querier_test.go
index 1e1d331487a..887725a9de4 100644
--- a/integration/querier_test.go
+++ b/integration/querier_test.go
@@ -71,7 +71,7 @@ func TestQuerierWithBlocksStorageRunningInMicroservicesMode(t *testing.T) {
 
 			// Configure the blocks storage to frequently compact TSDB head
 			// and ship blocks to the storage.
-			flags := mergeFlags(BlocksStorageFlags, map[string]string{
+			flags := mergeFlags(BlocksStorageFlags(), map[string]string{
 				"-blocks-storage.tsdb.block-ranges-period":         blockRangePeriod.String(),
 				"-blocks-storage.tsdb.ship-interval":               "1s",
 				"-blocks-storage.bucket-store.sync-interval":       "1s",
@@ -281,7 +281,7 @@ func TestQuerierWithBlocksStorageRunningInSingleBinaryMode(t *testing.T) {
 
 			// Configure the blocks storage to frequently compact TSDB head
 			// and ship blocks to the storage.
-			flags := mergeFlags(BlocksStorageFlags, map[string]string{
+			flags := mergeFlags(BlocksStorageFlags(), map[string]string{
 				"-blocks-storage.tsdb.block-ranges-period":                     blockRangePeriod.String(),
 				"-blocks-storage.tsdb.ship-interval":                           "1s",
 				"-blocks-storage.bucket-store.sync-interval":                   "1s",
@@ -423,7 +423,7 @@ func TestQuerierWithBlocksStorageOnMissingBlocksFromStorage(t *testing.T) {
 
 	// Configure the blocks storage to frequently compact TSDB head
 	// and ship blocks to the storage.
-	flags := mergeFlags(BlocksStorageFlags, map[string]string{
+	flags := mergeFlags(BlocksStorageFlags(), map[string]string{
 		"-blocks-storage.tsdb.block-ranges-period": blockRangePeriod.String(),
 		"-blocks-storage.tsdb.ship-interval":       "1s",
 		"-blocks-storage.tsdb.retention-period":    ((blockRangePeriod * 2) - 1).String(),
@@ -509,7 +509,7 @@ func TestQuerierWithChunksStorage(t *testing.T) {
 	defer s.Close()
 
 	require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
-	flags := mergeFlags(ChunksStorageFlags, map[string]string{})
+	flags := ChunksStorageFlags()
 
 	// Start dependencies.
 	dynamo := e2edb.NewDynamoDB()
@@ -517,7 +517,7 @@ func TestQuerierWithChunksStorage(t *testing.T) {
 	consul := e2edb.NewConsul()
 	require.NoError(t, s.StartAndWaitReady(consul, dynamo))
 
-	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
+	tableManager := e2ecortex.NewTableManager("table-manager", flags, "")
 	require.NoError(t, s.StartAndWaitReady(tableManager))
 
 	// Wait until the first table-manager sync has completed, so that we're
@@ -626,7 +626,7 @@ func TestHashCollisionHandling(t *testing.T) {
 	defer s.Close()
 
 	require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
-	flags := mergeFlags(ChunksStorageFlags, map[string]string{})
+	flags := ChunksStorageFlags()
 
 	// Start dependencies.
 	dynamo := e2edb.NewDynamoDB()
@@ -634,7 +634,7 @@ func TestHashCollisionHandling(t *testing.T) {
 	consul := e2edb.NewConsul()
 	require.NoError(t, s.StartAndWaitReady(consul, dynamo))
 
-	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
+	tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags(), "")
 	require.NoError(t, s.StartAndWaitReady(tableManager))
 
 	// Wait until the first table-manager sync has completed, so that we're
diff --git a/integration/query_frontend_test.go b/integration/query_frontend_test.go
index b9fe085e2a8..3eb91c4340f 100644
--- a/integration/query_frontend_test.go
+++ b/integration/query_frontend_test.go
@@ -29,10 +29,12 @@ type queryFrontendSetup func(t *testing.T, s *e2e.Scenario) (configFile string,
 
 func TestQueryFrontendWithBlocksStorageViaFlags(t *testing.T) {
 	runQueryFrontendTest(t, false, func(t *testing.T, s *e2e.Scenario) (configFile string, flags map[string]string) {
-		minio := e2edb.NewMinio(9000, BlocksStorageFlags["-blocks-storage.s3.bucket-name"])
+		flags = BlocksStorageFlags()
+
+		minio := e2edb.NewMinio(9000, flags["-blocks-storage.s3.bucket-name"])
 		require.NoError(t, s.StartAndWaitReady(minio))
 
-		return "", BlocksStorageFlags
+		return "", flags
 	})
 }
 
@@ -40,7 +42,7 @@ func TestQueryFrontendWithBlocksStorageViaConfigFile(t *testing.T) {
 	runQueryFrontendTest(t, false, func(t *testing.T, s *e2e.Scenario) (configFile string, flags map[string]string) {
 		require.NoError(t, writeFileToSharedDir(s, cortexConfigFile, []byte(BlocksStorageConfig)))
 
-		minio := e2edb.NewMinio(9000, BlocksStorageFlags["-blocks-storage.s3.bucket-name"])
+		minio := e2edb.NewMinio(9000, BlocksStorageFlags()["-blocks-storage.s3.bucket-name"])
 		require.NoError(t, s.StartAndWaitReady(minio))
 
 		return cortexConfigFile, e2e.EmptyFlags()
@@ -54,14 +56,15 @@ func TestQueryFrontendWithChunksStorageViaFlags(t *testing.T) {
 		dynamo := e2edb.NewDynamoDB()
 		require.NoError(t, s.StartAndWaitReady(dynamo))
 
-		tableManager := e2ecortex.NewTableManager("table-manager", ChunksStorageFlags, "")
+		flags = ChunksStorageFlags()
+		tableManager := e2ecortex.NewTableManager("table-manager", flags, "")
 		require.NoError(t, s.StartAndWaitReady(tableManager))
 
 		// Wait until the first table-manager sync has completed, so that we're
 		// sure the tables have been created.
 		require.NoError(t, tableManager.WaitSumMetrics(e2e.Greater(0), "cortex_table_manager_sync_success_timestamp_seconds"))
 
-		return "", ChunksStorageFlags
+		return "", flags
 	})
 }
 
@@ -86,7 +89,14 @@ func TestQueryFrontendWithChunksStorageViaConfigFile(t *testing.T) {
 
 func TestQueryFrontendTLSWithBlocksStorageViaFlags(t *testing.T) {
 	runQueryFrontendTest(t, false, func(t *testing.T, s *e2e.Scenario) (configFile string, flags map[string]string) {
-		minio := e2edb.NewMinio(9000, BlocksStorageFlags["-blocks-storage.s3.bucket-name"])
+		flags = mergeFlags(
+			BlocksStorageFlags(),
+			getServerTLSFlags(),
+			getClientTLSFlagsWithPrefix("ingester.client"),
+			getClientTLSFlagsWithPrefix("querier.frontend-client"),
+		)
+
+		minio := e2edb.NewMinio(9000, flags["-blocks-storage.s3.bucket-name"])
 		require.NoError(t, s.StartAndWaitReady(minio))
 
 		// set the ca
@@ -116,12 +126,7 @@ func TestQueryFrontendTLSWithBlocksStorageViaFlags(t *testing.T) {
 			filepath.Join(s.SharedDir(), serverKeyFile),
 		))
 
-		return "", mergeFlags(
-			BlocksStorageFlags,
-			getServerTLSFlags(),
-			getClientTLSFlagsWithPrefix("ingester.client"),
-			getClientTLSFlagsWithPrefix("querier.frontend-client"),
-		)
+		return "", flags
 	})
 }
 
diff --git a/integration/ruler_test.go b/integration/ruler_test.go
index 93f2400297a..023d61f4463 100644
--- a/integration/ruler_test.go
+++ b/integration/ruler_test.go
@@ -32,12 +32,12 @@ func TestRulerAPI(t *testing.T) {
 
 	// Start dependencies.
 	dynamo := e2edb.NewDynamoDB()
-	minio := e2edb.NewMinio(9000, RulerConfigs["-ruler.storage.s3.buckets"])
+	minio := e2edb.NewMinio(9000, RulerFlags()["-ruler.storage.s3.buckets"])
 	require.NoError(t, s.StartAndWaitReady(minio, dynamo))
 
 	// Start Cortex components.
 	require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
-	ruler := e2ecortex.NewRuler("ruler", mergeFlags(ChunksStorageFlags, RulerConfigs), "")
+	ruler := e2ecortex.NewRuler("ruler", mergeFlags(ChunksStorageFlags(), RulerFlags()), "")
 	require.NoError(t, s.StartAndWaitReady(ruler))
 
 	// Create a client with the ruler address configured
@@ -207,17 +207,17 @@ func TestRulerAlertmanager(t *testing.T) {
 
 	// Start dependencies.
 	dynamo := e2edb.NewDynamoDB()
-	minio := e2edb.NewMinio(9000, RulerConfigs["-ruler.storage.s3.buckets"])
+	minio := e2edb.NewMinio(9000, RulerFlags()["-ruler.storage.s3.buckets"])
 	require.NoError(t, s.StartAndWaitReady(minio, dynamo))
 
 	// Have at least one alertmanager configuration.
 	require.NoError(t, writeFileToSharedDir(s, "alertmanager_configs/user-1.yaml", []byte(cortexAlertmanagerUserConfigYaml)))
 
 	// Start Alertmanagers.
-	am1 := e2ecortex.NewAlertmanager("alertmanager1", mergeFlags(AlertmanagerFlags, AlertmanagerLocalFlags), "")
-	require.NoError(t, s.StartAndWaitReady(am1))
-	am2 := e2ecortex.NewAlertmanager("alertmanager2", mergeFlags(AlertmanagerFlags, AlertmanagerLocalFlags), "")
-	require.NoError(t, s.StartAndWaitReady(am2))
+	amFlags := mergeFlags(AlertmanagerFlags(), AlertmanagerLocalFlags())
+	am1 := e2ecortex.NewAlertmanager("alertmanager1", amFlags, "")
+	am2 := e2ecortex.NewAlertmanager("alertmanager2", amFlags, "")
+	require.NoError(t, s.StartAndWaitReady(am1, am2))
 
 	am1URL := "http://" + am1.HTTPEndpoint()
 	am2URL := "http://" + am2.HTTPEndpoint()
@@ -229,7 +229,7 @@ func TestRulerAlertmanager(t *testing.T) {
 
 	// Start Ruler.
 	require.NoError(t, writeFileToSharedDir(s, cortexSchemaConfigFile, []byte(cortexSchemaConfigYaml)))
-	ruler := e2ecortex.NewRuler("ruler", mergeFlags(ChunksStorageFlags, RulerConfigs, configOverrides), "")
+	ruler := e2ecortex.NewRuler("ruler", mergeFlags(ChunksStorageFlags(), RulerFlags(), configOverrides), "")
 	require.NoError(t, s.StartAndWaitReady(ruler))
 
 	// Create a client with the ruler address configured