Current approaches to designing energy-efficient applications typically rely on measuring individual components using readily available local metrics, like CPU utilization. However, these metrics fall short when applied to cloud-native applications, which operate within the multi-tenant, shared environments of distributed cloud providers. Assessing and optimizing the energy efficiency of cloud-native applications requires consideration of the complex, layered nature of modern cloud stacks. To address this need, we present a comprehensive, automated, and extensible experimentation framework that enables developers to measure energy efficiency across all relevant layers of a cloud-based application and evaluate associated quality trade-offs. Our framework integrates a suite of service quality and sustainability metrics, providing compatibility with any Kubernetes-based application. We demonstrate the feasibility and effectiveness of this approach through initial experimental results, comparing architectural design alternatives for a widely used open-source cloud-native application.