Most difficult part of interoperability in PON is management of the network. Different types of PON use different management tools, such as OMCI (ONT management and control interface) for GPON and MPCP (MultiPoint Control Protocol) for the EPON. Since both of the tools use frames for management information transportation, interoperability test must be able to extract and analyse those frames from the data traffic. The management frames are tested to ensure the vendor-defined resource allocation algorithms are operating properly. Deeper interoperability evaluation will require additional tests.

Another challenging interoperability test is the QoS testing. QoS differ from product to product, having different queue management schemes and diverse scheduling schemes. Since there is so many differences in different devices, testing might be challenging.