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The interest in electric and hybrid electric power system has been increasing, in recent times, due to the benefits of this technology, such as high power-to-weight ratio, reliability, compactness, quietness, and, above all, elimination of local pollutant emissions. One of the key factors of these technologies is the possibility to exploit the synergy between powertrain, structure, and mission. This investigation addresses this topic by applying multi-objective optimization to two test cases—a fixed-wing, tail-sitter, Vertical Take-off and Landing Unmanned Aerial Vehicle (VTOL-UAV), and a Medium-Altitude Long-Endurance Unmanned Aerial Vehicle (MALE-UAV). Cruise time and payload weight were selected as goals for the first optimization problem, while fuel consumption and electric endurance were selected for the second one. The optimizations were performed with Non-dominated Sorting Genetic Algorithm-II (NSGA-II) and S-Metric Selection Evolutionary Multiobjective Algorithm (SMS-EMOA), by taking several constraints into account. The VTOL-UAV optimization was performed, at different levels (structure only, power system only, structure and power system together). To better underline the synergic effect of electrification, the potential benefit of structural integration and multi-functionalization was also addressed. The optimization of the MALE-UAV was performed at two different levels (power system only, power system, and mission profile together), to explore the synergic effect of hybridization. Results showed that large improvements could be obtained, either in the first test case when, both, the powertrain design and the aircraft structure were considered, and in the optimization of the hybrid electric UAV, where the optimization of the aircraft flight path gave a strong contribution to the overall performances.