diff --git a/deploy/charts/harvester/templates/configmap.yaml b/deploy/charts/harvester/templates/configmap.yaml
index 8b0d06407fd..55cbf471959 100644
--- a/deploy/charts/harvester/templates/configmap.yaml
+++ b/deploy/charts/harvester/templates/configmap.yaml
@@ -69,6 +69,15 @@ data:
     audit-policy-file: /etc/rancher/rke2/config.yaml.d/92-harvester-kube-audit-policy.yaml
     EOF
 
+    # Disable snapshot-controller related charts because we manage them in Harvester.
+    # RKE2 enables these charts by default after v1.25.7 (https://github.com/rancher/rke2/releases/tag/v1.25.7%2Brke2r1)
+    cat > /host/etc/rancher/rke2/config.yaml.d/40-disable-charts.yaml <<EOF
+    disable:
+    - rke2-snapshot-controller
+    - rke2-snapshot-controller-crd
+    - rke2-snapshot-validation-webhook
+    EOF
+
     # For how to promote nodes, see: https://github.com/rancher/rancher/issues/36480#issuecomment-1039253499
     ROLE_LABELS="rke.cattle.io/control-plane-role=true rke.cattle.io/etcd-role=true"
     $KUBECTL label --overwrite -n fleet-local machines.cluster.x-k8s.io $CUSTOM_MACHINE $ROLE_LABELS
diff --git a/package/upgrade/upgrade_node.sh b/package/upgrade/upgrade_node.sh
index 9ed637a8ab4..e2ca33e7379 100755
--- a/package/upgrade/upgrade_node.sh
+++ b/package/upgrade/upgrade_node.sh
@@ -387,6 +387,7 @@ command_pre_drain() {
   patch_logging_event_audit
 
   remove_rke2_canal_config
+  disable_rke2_charts
 }
 
 get_node_rke2_version() {
@@ -428,6 +429,17 @@ remove_rke2_canal_config() {
   rm -f "$HOST_DIR/var/lib/rancher/rke2/server/manifests/rke2-canal-config.yaml"
 }
 
+# Disable snapshot-controller related charts because we manage them in Harvester.
+# RKE2 enables these charts by default after v1.25.7 (https://github.com/rancher/rke2/releases/tag/v1.25.7%2Brke2r1)
+disable_rke2_charts() {
+  cat > "$HOST_DIR/etc/rancher/rke2/config.yaml.d/40-disable-charts.yaml" <<EOF
+disable:
+- rke2-snapshot-controller
+- rke2-snapshot-controller-crd
+- rke2-snapshot-validation-webhook
+EOF
+}
+
 convert_nodenetwork_to_vlanconfig() {
   # sometimes (e.g. apiserver is busy/not ready), the kubectl may fail, use the saved value
   if [ -z "$UPGRADE_PREVIOUS_VERSION" ]; then
@@ -587,6 +599,7 @@ command_single_node_upgrade() {
   detect_repo
 
   remove_rke2_canal_config
+  disable_rke2_charts
 
   # Copy OS things, we need to shutdown repo VMs.
   NEW_OS_SQUASHFS_IMAGE_FILE=$(mktemp -p $UPGRADE_TMP_DIR)