Existing Building Automation Systems (BASs) and Building Automation Networks (BANs) have been shown to have serious cybersecurity problems. Due to the safety-critical and interconnected nature of building subsystems, local and network access control needs to be finer grained, taking into consideration the varying criticality of applications running on heterogeneous devices. In this paper, we present a secure communication framework for BASs that 1) enforces rich access control policy for operating system services and objects, leveraging a microkernel-based architecture; 2) supports fine-grained network access control on a per-process basis; 3) unifies the security control of inter-device and intra-device communication using proxy processes; 4) tunnels legacy insecure communication protocols (e.g., BACnet) through a secure channel, such as SSL, in a manner transparent to legacy applications. We implemented the framework on seL4, a formally verified microkernel. We conducted extensive experiments and analysis to compare the performance and effectiveness of our communication systems against a traditional Linux-based implementation of the same control scenario. Our experiments show that the communication performance of our system is faster or comparable to the Linux-based architecture in embedded systems.