Kubernetes has become the dominant platform for managing containerized applications, but its native Secrets management mechanisms introduce security vulnerabilities, especially in environments where third-party applications may have excessive permissions. In this paper, we present KubeKeeper, a comprehensive solution for protecting Kubernetes Secrets against leakage due to excessive permissions. KubeKeeper automatically encrypts Secrets and ensures that only explicitly authorized Pods can access their decrypted form. This is achieved by integrating with Kubernetes’ admission control framework to transparently enforce access policies, without requiring changes to application code and with minimal integration effort into existing cluster infrastructure. We evaluated KubeKeeper on a diverse set of 498 Kubernetes applications and demonstrate that it successfully protects Secrets against all identified excessive permissions, without introducing performance degradation during execution or any significant overhead during Pod creation and deployment.