In recent years, residential users have begun to be equipped with micro-CHP (combined heat and power) generation technologies with the aim of decreasing primary energy consumption and reducing environmental impact. In these systems, the prime mover supplies both thermal and electrical energy, and an auxiliary boiler and the national electrical grid are employed as supplementary systems. In this paper, a simulation model, which accounts for component efficiency and energy balance, was developed to replicate the interaction between the users and the energy systems in order to minimize primary energy consumption. The simulation model identified the optimal operation strategy of two residential users by investigating different energy system configurations by means of a dynamic programming algorithm. The reference scenario was compared to three different scenarios by considering independent energy systems, shared thermal and electrical energy storage and also the shared prime mover. Such a comparison allowed the identification of the most suitable energy system configuration and optimized operation strategy. The results demonstrate that the optimized operation strategy smoothes the influence of the size of thermal and electrical energy storage. Moreover, the saving of primary energy consumption can be as high as 5.1%. The analysis of the economic feasibility reveals that the investment cost of the prime mover can be as high as 4000 €/kW.