diff --git a/charts/kube-prometheus-stack/Chart.yaml b/charts/kube-prometheus-stack/Chart.yaml
index a16daf8d8a17..091debb25b94 100644
--- a/charts/kube-prometheus-stack/Chart.yaml
+++ b/charts/kube-prometheus-stack/Chart.yaml
@@ -22,7 +22,7 @@ name: kube-prometheus-stack
 sources:
   - https://github.com/prometheus-community/helm-charts
   - https://github.com/prometheus-operator/kube-prometheus
-version: 40.3.1
+version: 40.4.0
 appVersion: 0.59.2
 kubeVersion: ">=1.16.0-0"
 home: https://github.com/prometheus-operator/kube-prometheus
diff --git a/charts/kube-prometheus-stack/templates/thanos-ruler/ruler.yaml b/charts/kube-prometheus-stack/templates/thanos-ruler/ruler.yaml
index 1f294f8dc990..73d5a7d6de0b 100644
--- a/charts/kube-prometheus-stack/templates/thanos-ruler/ruler.yaml
+++ b/charts/kube-prometheus-stack/templates/thanos-ruler/ruler.yaml
@@ -78,6 +78,10 @@ spec:
   queryEndpoints:
 {{ toYaml .Values.thanosRuler.thanosRulerSpec.queryEndpoints | indent 4 }}
 {{- end }}
+{{- if .Values.thanosRuler.thanosRulerSpec.queryConfig }}
+  queryConfig:
+{{ toYaml .Values.thanosRuler.thanosRulerSpec.queryConfig | indent 4 }}
+{{- end }}
 {{- if .Values.thanosRuler.thanosRulerSpec.resources }}
   resources:
 {{ toYaml .Values.thanosRuler.thanosRulerSpec.resources | indent 4 }}
diff --git a/charts/kube-prometheus-stack/values.yaml b/charts/kube-prometheus-stack/values.yaml
index ce3e59d63fe8..62397399a3eb 100644
--- a/charts/kube-prometheus-stack/values.yaml
+++ b/charts/kube-prometheus-stack/values.yaml
@@ -3261,6 +3261,14 @@ thanosRuler:
     ## When used alongside with ObjectStorageConfig, ObjectStorageConfigFile takes precedence.
     objectStorageConfigFile: ""
 
+    ## QueryEndpoints defines Thanos querier endpoints from which to query metrics.
+    ## Maps to the --query flag of thanos ruler.
+    queryEndpoints: []
+
+    ## Define configuration for connecting to thanos query instances. If this is defined, the queryEndpoints field will be ignored.
+    ## Maps to the query.config CLI argument. Only available with thanos v0.11.0 and higher.
+    queryConfig: {}
+
     ## Labels configure the external label pairs to ThanosRuler. A default replica
     ## label `thanos_ruler_replica` will be always added as a label with the value
     ## of the pod's name and it will be dropped in the alerts.