diff --git a/test/endtoend/operator/cluster_upgrade.yaml b/test/endtoend/operator/cluster_upgrade.yaml
index 2aa0e229..72831d35 100644
--- a/test/endtoend/operator/cluster_upgrade.yaml
+++ b/test/endtoend/operator/cluster_upgrade.yaml
@@ -85,6 +85,13 @@ spec:
                   cpu: 100m
                   memory: 512Mi
               configOverrides: "innodb_fast_shutdown=0"
+            # Configure extra flags for mysqld_exporter and check them in the upgrade test
+            mysqldExporter:
+              extraFlags:
+                collect.info_schema.tables.databases: "*" # Override operator default
+                collect.info_schema.innodb_cmpmem: "true" # Duplicate flag, overriden below
+                collect.info_schema.innodb_cmpmem: "false"
+                collect.info_schema.tables: "true"
             dataVolumeClaimTemplate:
               accessModes: ["ReadWriteOnce"]
               resources:
diff --git a/test/endtoend/upgrade_test.sh b/test/endtoend/upgrade_test.sh
index f1c47413..cafa3b27 100755
--- a/test/endtoend/upgrade_test.sh
+++ b/test/endtoend/upgrade_test.sh
@@ -232,6 +232,15 @@ COrder
 EOF
 }
 
+function verifyResourceSpec() {
+  echo "Verifying resource spec"
+
+  echo "mysqld_exporter flags:"
+  checkPodSpecBySelectorWithTimeout "planetscale.com/component=vttablet" 3 "--no-collect.info_schema.innodb_cmpmem$"
+  checkPodSpecBySelectorWithTimeout "planetscale.com/component=vttablet" 3 "--collect.info_schema.tables$"
+  checkPodSpecBySelectorWithTimeout "planetscale.com/component=vttablet" 3 "--collect.info_schema.tables.databases=\*$"
+}
+
 # Test setup
 echo "Building the docker image"
 docker build -f build/Dockerfile.release -t vitess-operator-pr:latest .
@@ -251,6 +260,7 @@ checkSemiSyncSetup
 verifyDurabilityPolicy "commerce" "semi_sync"
 upgradeToLatest
 verifyVtGateVersion "22.0.0"
+verifyResourceSpec
 checkSemiSyncSetup
 # After upgrading, we verify that the durability policy is still semi_sync
 verifyDurabilityPolicy "commerce" "semi_sync"