diff --git a/kubernetes/apps/network/cloudflare-ddns/ks.yaml b/kubernetes/apps/network/cloudflare-ddns/ks.yaml
index 31142fa961b19..2335ec30c452c 100644
--- a/kubernetes/apps/network/cloudflare-ddns/ks.yaml
+++ b/kubernetes/apps/network/cloudflare-ddns/ks.yaml
@@ -13,7 +13,7 @@ spec:
   dependsOn:
     - name: external-secrets-stores
   path: ./kubernetes/apps/network/cloudflare-ddns/app
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
diff --git a/kubernetes/apps/network/cloudflared/ks.yaml b/kubernetes/apps/network/cloudflared/ks.yaml
index 188328eb3d15f..8dd7bb80886d8 100644
--- a/kubernetes/apps/network/cloudflared/ks.yaml
+++ b/kubernetes/apps/network/cloudflared/ks.yaml
@@ -14,7 +14,7 @@ spec:
     - name: external-dns-cloudflare
     - name: external-secrets-stores
   path: ./kubernetes/apps/network/cloudflared/app
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
diff --git a/kubernetes/apps/network/echo-server/ks.yaml b/kubernetes/apps/network/echo-server/ks.yaml
index b3d6987fce7a3..8a9de4638f231 100644
--- a/kubernetes/apps/network/echo-server/ks.yaml
+++ b/kubernetes/apps/network/echo-server/ks.yaml
@@ -11,7 +11,7 @@ spec:
     labels:
       app.kubernetes.io/name: *app
   path: ./kubernetes/apps/network/echo-server/app
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
diff --git a/kubernetes/apps/network/external-dns/ks.yaml b/kubernetes/apps/network/external-dns/ks.yaml
index a6372cc1dadf4..9c19d7e9c597d 100644
--- a/kubernetes/apps/network/external-dns/ks.yaml
+++ b/kubernetes/apps/network/external-dns/ks.yaml
@@ -13,7 +13,7 @@ spec:
   dependsOn:
     - name: external-secrets-stores
   path: ./kubernetes/apps/network/external-dns/cloudflare
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
@@ -35,10 +35,10 @@ spec:
   dependsOn:
     - name: external-secrets-stores
   path: ./kubernetes/apps/network/external-dns/unifi
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
-  wait: true
+  wait: false
   interval: 30m
   timeout: 5m
diff --git a/kubernetes/apps/network/nginx/ks.yaml b/kubernetes/apps/network/nginx/ks.yaml
index 208a0041db395..a1f03f09d7b21 100644
--- a/kubernetes/apps/network/nginx/ks.yaml
+++ b/kubernetes/apps/network/nginx/ks.yaml
@@ -14,7 +14,7 @@ spec:
     - name: cert-manager-issuers
     - name: external-secrets-stores
   path: ./kubernetes/apps/network/nginx/certificates
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
@@ -37,7 +37,7 @@ spec:
     - name: external-secrets-stores
     - name: nginx-certificates
   path: ./kubernetes/apps/network/nginx/external
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
@@ -59,7 +59,7 @@ spec:
   dependsOn:
     - name: nginx-certificates
   path: ./kubernetes/apps/network/nginx/internal
-  prune: false
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system
diff --git a/kubernetes/apps/observability/silence-operator/ks.yaml b/kubernetes/apps/observability/silence-operator/ks.yaml
index 16f86b678b892..db2a61fd115dd 100644
--- a/kubernetes/apps/observability/silence-operator/ks.yaml
+++ b/kubernetes/apps/observability/silence-operator/ks.yaml
@@ -31,7 +31,7 @@ spec:
     labels:
       app.kubernetes.io/name: *app
   path: ./kubernetes/apps/observability/silence-operator/crds
-  prune: false # never should be deleted
+  prune: true
   sourceRef:
     kind: GitRepository
     name: flux-system