diff --git a/manifest/overlays/production/kustomization.yaml b/manifest/overlays/production/kustomization.yaml
index 1543256..e7e3004 100644
--- a/manifest/overlays/production/kustomization.yaml
+++ b/manifest/overlays/production/kustomization.yaml
@@ -5,12 +5,9 @@ namespace: toolhive-system
 
 resources:
   - mcp-kube-rbac.yaml
-  - mcpserver-gitea.yaml
-  - mcpserver-radar.yaml
-  - mcpserver-argocd.yaml
-  - mcpserver-kubernetes.yaml
-  - mcp-headless-services.yaml
-  - mcp-group-homelab-core.yaml
+  - mcp-servers/
+  - registry/
+  - vmcp-servers/
   - ingressroute.yaml
   - secrets/gitea-mcp-secret.sealed.secret.yaml
   - secrets/argocd-mcp-secret.sealed.secret.yaml
@@ -18,13 +15,4 @@ resources:
   - mcp-tool-config-ops.yaml
   - mcp-tool-config-dev.yaml
   - embedding-server.yaml
-  - full-vmcp.yaml
-  - full-vmcp-ingress.yaml
-  - dev-safe-vmcp.yaml
-  - dev-safe-vmcp-ingress.yaml
-  - ops-safe-vmcp.yaml
-  - ops-safe-vmcp-ingress.yaml
-  - k8s-registry.yaml
-  - k8s-registry-rbac.yaml
-  - toolhive-registry-backup.yaml
-  - toolhive-registry-postgres.yaml
+
diff --git a/manifest/overlays/production/mcp-servers/kustomization.yaml b/manifest/overlays/production/mcp-servers/kustomization.yaml
new file mode 100644
index 0000000..898cd05
--- /dev/null
+++ b/manifest/overlays/production/mcp-servers/kustomization.yaml
@@ -0,0 +1,10 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+namespace: toolhive-system
+
+resources:
+  - mcpserver-gitea.yaml
+  - mcpserver-radar.yaml
+  - mcpserver-argocd.yaml
+  - mcpserver-kubernetes.yaml
diff --git a/manifest/overlays/production/mcpserver-argocd.yaml b/manifest/overlays/production/mcp-servers/mcpserver-argocd.yaml
similarity index 100%
rename from manifest/overlays/production/mcpserver-argocd.yaml
rename to manifest/overlays/production/mcp-servers/mcpserver-argocd.yaml
diff --git a/manifest/overlays/production/mcpserver-gitea.yaml b/manifest/overlays/production/mcp-servers/mcpserver-gitea.yaml
similarity index 100%
rename from manifest/overlays/production/mcpserver-gitea.yaml
rename to manifest/overlays/production/mcp-servers/mcpserver-gitea.yaml
diff --git a/manifest/overlays/production/mcpserver-kubernetes.yaml b/manifest/overlays/production/mcp-servers/mcpserver-kubernetes.yaml
similarity index 100%
rename from manifest/overlays/production/mcpserver-kubernetes.yaml
rename to manifest/overlays/production/mcp-servers/mcpserver-kubernetes.yaml
diff --git a/manifest/overlays/production/mcpserver-radar.yaml b/manifest/overlays/production/mcp-servers/mcpserver-radar.yaml
similarity index 100%
rename from manifest/overlays/production/mcpserver-radar.yaml
rename to manifest/overlays/production/mcp-servers/mcpserver-radar.yaml
diff --git a/manifest/overlays/production/k8s-registry-rbac.yaml b/manifest/overlays/production/registry/k8s-registry-rbac.yaml
similarity index 100%
rename from manifest/overlays/production/k8s-registry-rbac.yaml
rename to manifest/overlays/production/registry/k8s-registry-rbac.yaml
diff --git a/manifest/overlays/production/k8s-registry.yaml b/manifest/overlays/production/registry/k8s-registry.yaml
similarity index 100%
rename from manifest/overlays/production/k8s-registry.yaml
rename to manifest/overlays/production/registry/k8s-registry.yaml
diff --git a/manifest/overlays/production/registry/kustomization.yaml b/manifest/overlays/production/registry/kustomization.yaml
new file mode 100644
index 0000000..6441567
--- /dev/null
+++ b/manifest/overlays/production/registry/kustomization.yaml
@@ -0,0 +1,10 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+namespace: toolhive-system
+
+resources:
+  - k8s-registry.yaml
+  - k8s-registry-rbac.yaml
+  - toolhive-registry-backup.yaml
+  - toolhive-registry-postgres.yaml
diff --git a/manifest/overlays/production/toolhive-registry-backup.yaml b/manifest/overlays/production/registry/toolhive-registry-backup.yaml
similarity index 100%
rename from manifest/overlays/production/toolhive-registry-backup.yaml
rename to manifest/overlays/production/registry/toolhive-registry-backup.yaml
diff --git a/manifest/overlays/production/toolhive-registry-postgres.yaml b/manifest/overlays/production/registry/toolhive-registry-postgres.yaml
similarity index 100%
rename from manifest/overlays/production/toolhive-registry-postgres.yaml
rename to manifest/overlays/production/registry/toolhive-registry-postgres.yaml
diff --git a/manifest/overlays/production/dev-safe-vmcp-ingress.yaml b/manifest/overlays/production/vmcp-servers/dev-safe-vmcp-ingress.yaml
similarity index 100%
rename from manifest/overlays/production/dev-safe-vmcp-ingress.yaml
rename to manifest/overlays/production/vmcp-servers/dev-safe-vmcp-ingress.yaml
diff --git a/manifest/overlays/production/dev-safe-vmcp.yaml b/manifest/overlays/production/vmcp-servers/dev-safe-vmcp.yaml
similarity index 100%
rename from manifest/overlays/production/dev-safe-vmcp.yaml
rename to manifest/overlays/production/vmcp-servers/dev-safe-vmcp.yaml
diff --git a/manifest/overlays/production/full-vmcp-ingress.yaml b/manifest/overlays/production/vmcp-servers/full-vmcp-ingress.yaml
similarity index 100%
rename from manifest/overlays/production/full-vmcp-ingress.yaml
rename to manifest/overlays/production/vmcp-servers/full-vmcp-ingress.yaml
diff --git a/manifest/overlays/production/full-vmcp.yaml b/manifest/overlays/production/vmcp-servers/full-vmcp.yaml
similarity index 100%
rename from manifest/overlays/production/full-vmcp.yaml
rename to manifest/overlays/production/vmcp-servers/full-vmcp.yaml
diff --git a/manifest/overlays/production/vmcp-servers/kustomization.yaml b/manifest/overlays/production/vmcp-servers/kustomization.yaml
new file mode 100644
index 0000000..456fb29
--- /dev/null
+++ b/manifest/overlays/production/vmcp-servers/kustomization.yaml
@@ -0,0 +1,12 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+namespace: toolhive-system
+
+resources:
+  - full-vmcp.yaml
+  - full-vmcp-ingress.yaml
+  - dev-safe-vmcp.yaml
+  - dev-safe-vmcp-ingress.yaml
+  - ops-safe-vmcp.yaml
+  - ops-safe-vmcp-ingress.yaml
diff --git a/manifest/overlays/production/ops-safe-vmcp-ingress.yaml b/manifest/overlays/production/vmcp-servers/ops-safe-vmcp-ingress.yaml
similarity index 100%
rename from manifest/overlays/production/ops-safe-vmcp-ingress.yaml
rename to manifest/overlays/production/vmcp-servers/ops-safe-vmcp-ingress.yaml
diff --git a/manifest/overlays/production/ops-safe-vmcp.yaml b/manifest/overlays/production/vmcp-servers/ops-safe-vmcp.yaml
similarity index 100%
rename from manifest/overlays/production/ops-safe-vmcp.yaml
rename to manifest/overlays/production/vmcp-servers/ops-safe-vmcp.yaml