diff --git a/charts/kube-prometheus-stack/templates/thanos-ruler/secret.yaml b/charts/kube-prometheus-stack/templates/thanos-ruler/secret.yaml
index ddd6f25e74c0..acab7fd9aeda 100644
--- a/charts/kube-prometheus-stack/templates/thanos-ruler/secret.yaml
+++ b/charts/kube-prometheus-stack/templates/thanos-ruler/secret.yaml
@@ -8,13 +8,19 @@ metadata:
     app: {{ include "kube-prometheus-stack.thanosRuler.name" . }}
 {{ include "kube-prometheus-stack.labels" . | indent 4 }}
 data:
-{{- if .Values.thanosRuler.thanosRulerSpec.alertmanagersConfig.secret }}
-  alertmanager-configs.yaml: {{ toYaml .Values.thanosRuler.thanosRulerSpec.alertmanagersConfig.secret | b64enc | quote }}
-{{- end }}
-{{- if .Values.thanosRuler.thanosRulerSpec.objectStorageConfig.secret }}
-  object-storage-configs.yaml: {{ toYaml .Values.thanosRuler.thanosRulerSpec.objectStorageConfig.secret | b64enc | quote }}
-{{- end }}
-{{- if .Values.thanosRuler.thanosRulerSpec.queryConfig.secret }}
-  query-configs.yaml: {{ toYaml .Values.thanosRuler.thanosRulerSpec.queryConfig.secret | b64enc | quote }}
-{{- end }}
+  {{- with .Values.thanosRuler.thanosRulerSpec.alertmanagersConfig }}
+  {{- if and .secret (not .existingSecret) }}
+  alertmanager-configs.yaml: {{ toYaml .secret | b64enc | quote }}
+  {{- end }}
+  {{- end }}
+  {{- with .Values.thanosRuler.thanosRulerSpec.objectStorageConfig }}
+  {{- if and .secret (not .existingSecret) }}
+  object-storage-configs.yaml: {{ toYaml .secret | b64enc | quote }}
+  {{- end }}
+  {{- end }}
+  {{- with .Values.thanosRuler.thanosRulerSpec.queryConfig }}
+  {{- if and .secret (not .existingSecret) }}
+  query-configs.yaml: {{ toYaml .secret | b64enc | quote }}
+  {{- end }}
+  {{- end }}
 {{- end }}
diff --git a/charts/kube-prometheus-stack/values.yaml b/charts/kube-prometheus-stack/values.yaml
index 650d358e8ab8..6368d75e7bd3 100644
--- a/charts/kube-prometheus-stack/values.yaml
+++ b/charts/kube-prometheus-stack/values.yaml
@@ -3966,7 +3966,7 @@ thanosRuler:
       existingSecret: {}
         # name: ""
         # key: ""
-      # will render alertmanagersConfig
+      # will render render alertmanagersConfig secret data and configure it to be used by Thanos Ruler custom resource, ignored when alertmanagersConfig.existingSecret is set
       # https://thanos.io/tip/components/rule.md/#alertmanager
       secret: {}
         # alertmanagers:
@@ -4000,7 +4000,7 @@ thanosRuler:
       existingSecret: {}
         # name: ""
         # key: ""
-      # will render objectStorageConfig
+      # will render objectStorageConfig secret data and configure it to be used by Thanos Ruler custom resource, ignored when alertmanagersConfig.existingSecret is set
       # https://thanos.io/tip/thanos/storage.md/#s3
       secret: {}
         # type: S3
@@ -4026,7 +4026,7 @@ thanosRuler:
       existingSecret: {}
         # name: ""
         # key: ""
-      # will render queryConfig
+      # render queryConfig secret data and configure it to be used by Thanos Ruler custom resource, ignored when queryConfig.existingSecret is set
       # https://thanos.io/tip/components/rule.md/#query-api
       secret: {}
         # - http_config: