Wireless sensor networks (WSNs) as a central part of cyber-physical systems are gaining commercial momentum in many areas, including building monitoring and intelligent home automation. Users wish to successively deploy hardware from different vendors. Interoperability is taken for granted by the customers who want to avoid the need for exhaustive configuration and set-up. Therefore, the need for an interoperable and efficient application layer protocol for machine-to-machine communication in and across the boundaries of WSNs arises. We address these issues with our implementation of TinyIPFIX, an adaption of the IP Flow Information Export (IPFIX) protocol. Throughout the paper we show how to leverage TinyIPFIX in the context of an office scenario and we discuss how the protocol may be applied to other significant WSN deployments presented in literature over the past few years. This article additionally shows how to improve the functionality of TinyIPFIX by adding both syntactic and semantic aggregation functionality to the established system. Finally, we evaluate the performance of TinyIPFIX in a large test bed with over 40 motes running TinyOS and analyze TinyIPFIX’s system performance in comparison with previous approaches.