Microservices have become promising candidates for the deployment of network and vertical functions in the fifth generation of mobile networks. However, microservice platforms like Kubernetes use a flat networking approach towards the connectivity of virtualised workloads, which prevents the deployment of network functions on isolated network segments (for example, the components of an IP Telephony system or a content distribution network). This paper presents L2S-M, a solution that enables the connectivity of Kubernetes microservices over isolated link-layer virtual networks, regardless of the compute nodes where workloads are actually deployed. L2S-M uses software-defined networking (SDN) to fulfil this purpose. Furthermore, the L2S-M design is flexible to support the connectivity of Kubernetes workloads across different Kubernetes clusters. We validate the functional behaviour of our solution in a moderately complex Smart Campus scenario, where L2S-M is used to deploy a content distribution network, showing its potential for the deployment of network services in distributed and heterogeneous environments.