During the last few years, attention has overwhelmingly focused on the integrated management of urban services and the demand of customers for locally-based supply. The rapid growth in developing smart measuring devices has made the underlying systems more observable and controllable. This exclusive feature has led the system designers to pursue the implementation of complex protocols to provide faster services based on data exchanges. On the other hand, the demands of consumers for locally-based supply could cause a disjunction and islanding behavior that demands to be dealt with by precise action. At first, keeping a centralization scheme was the main priority. However, the advent of distributed systems opened up new solutions. The operation of distributed systems requires the implementation of strong communication links to boost the existing infrastructure via smart control and supervision, which requires a foundation and effective investigations. Hence, necessary actions need to be taken to frustrate any disruptive penetrations into the system while simultaneously benefiting from the advantages of the proposed smart platform. This research addresses the detection of false data injection attacks (FDIA) in energy hub systems. Initially, a multi-hub system both in the presence of a microgrid (the interconnected smart energy hub-based microgrid system) and without it has been modeled for energy management in a way that allows them to cooperate toward providing energy with each other. Afterward, an FDIA is separately exerted to all three parts of the energy carrier including the thermal, water, and electric systems. In the absence of FDIA detection, the impact of FDIA is thoroughly illustrated on energy management, which considerably contributes to non-optimal operation. In the same vein, the intelligent priority selection based reinforcement learning (IPS-RL) method is proposed for FDIA detection. In order to model the uncertainty effects, the unscented transformation (UT) is applied in a stochastic framework. The results on the IEEE standard test system validate the system’s performance.