This study explores the integration of Kubernetes with embedded systems in the Internet of Medical Things, focusing on enhancing security through post-quantum cryptography (PQC). It leverages the CRYSTAL-Kyber algorithm and ASCON to fortify IoMT against quantum computing threats while maintaining operational efficiency. The urgency of this research escalates with the advancements in quantum computing. Performance evaluations show Kyber512's key encapsulation at 3,464 mu s and decryption at 3,844 mu s, indicating suitability for time-sensitive medical applications. Additionally, the research investigates cryptographic scalability with Docker and Kubernetes to achieve a balance of security, flexibility, and scalability essential for IoMT's reliable operation in healthcare contexts. Resource efficiency is highlighted with CPU usage on a Raspberry Pi master node at 8% without workload pods and memory usage increasing from 36% to 69% when scaling from zero to four pods, showcasing Kubernetes's ability to manage cryptographic operations efficiently. The findings affirm the benefits of integrating post-quantum and lightweight cryptographic techniques within a Kubernetes-managed IoMT framework. Low CPU usage across nodes, even under multiple pods, demonstrates the system's capacity to handle increased workloads effectively, offering robust protection against quantum threats without compromising performance. This integration presents a viable strategy to enhance IoMT security and efficiency amidst growing quantum computing challenges.