Integration of different networks enhances sustainable applications but specific vulnerabilities must be faced up too. New network components often are introduced to efficiently adapt different technologies, whereas in some cases they can be exploited as sources for generation of anomalous events in the interconnected networks attributable to security attacks. This paper deals with security for heterogeneous and inter-operable communication networks including a satellite segment, focusing on the application of an Intrusion Detection System (IDS) on the target scenario. The baseline envisages the presence of Performance Enhancing Proxies (PEPs) at the edges of satellite links, which implies the twofold effect of improving TCP performance but also increasing a PEP-related vulnerability due to the violation of the end-to-end semantic of TCP. The paper addresses the above mentioned issue through the realization of a test bed including a real geostationary satellite link operated by Telespazio. Outcomes of experiments show the effectiveness of the application of the proposed IDS system.