diff --git a/src/main/java/com/aws/greengrass/deployment/bootstrap/BootstrapManager.java b/src/main/java/com/aws/greengrass/deployment/bootstrap/BootstrapManager.java
index 183d710a79..018386fa5e 100644
--- a/src/main/java/com/aws/greengrass/deployment/bootstrap/BootstrapManager.java
+++ b/src/main/java/com/aws/greengrass/deployment/bootstrap/BootstrapManager.java
@@ -161,6 +161,7 @@ public boolean isBootstrapRequired(Map<String, Object> newConfig)
     private boolean willRemovePlugins(Map<String, Object> serviceConfig) {
         Set<String> pluginsToRemove = kernel.orderedDependencies().stream()
                 .filter(s -> s instanceof PluginService)
+                .filter(s -> !s.isBuiltin())
                 .filter(s -> !serviceConfig.containsKey(s.getName()))
                 .map(GreengrassService::getName)
                 .collect(Collectors.toSet());