Hybrid energy systems combine multiple energy sources and storage technologies to enhance performance and meet diverse energy needs. Hybrid heat pump systems are particularly suitable for heating and cooling buildings in rural areas. Air-source heat pumps have two well-known disadvantages during the coldest period of the year, when the building’s heating load is at its peak: the heat pump’s capacity is reduced and it needs to perform defrost cycles. A potential solution is to size the heat pump to cover only a portion of the peak load and to use a second heat generator in a hybrid heat pump system. There is a gap in the literature regarding the configurational analysis of hybrid heat pump (HHP) systems, particularly in terms of combining heat pumps and biomass boilers, and evaluating their efficiency, economic aspects, and environmental impact. Thus, in this research, a dynamic model of a HHP system, consisting of an air-to-water heat pump paired with a biomass boiler as a backup, is presented. Various configurations of the HHP system have been developed to evaluate key performance indicators, such as efficiency, emissions, operational costs, and other relevant factors. The findings of this paper indicate that the energy performance of HHP systems is significantly affected by the system layout, heat pump size, cut-off temperature, and the control algorithm used to activate the heat generators. Moreover, series operation of HHP systems is not only more efficient than parallel operation but also results in lower emissions and reduced operation costs. As expected, the energy loss associated with defrost cycles significantly impacts the overall performance of a hybrid system based on an air-source heat pump. Finally, the impact of the cut-off temperature on the key parameters in the configuration analysis was examined, and the optimal performance of the HHP system, in terms of minimizing operational costs and emissions, was depicted using a heat map diagram.