A retrofit analysis on a 90 passengers regional jet aircraft is performed through a multidisciplinary collaborative aircraft design and optimization highlighting the impact on costs and performance. Two different activities are accounted for selecting the best aircraft retrofit solution: a re-engining operation that allows to substitute a conventional power-plant platform with advanced geared turbofan and an on-board-systems architecture modernization, considering different levels of electrification. Besides the variables that are directly dependent from these activities, also scenario variables are considered during the optimization such as the fuel price, the fleet size and the years of utilization of the upgraded systems. The optimization is led by impacts of the retrofitting process on emissions, capital costs and saving costs, computed at industrial level. Overall aircraft design competences (aerodynamics, masses, performance, noise, and emissions) have been computed increasing the level of fidelity and reliability. The whole process is implemented in the framework of the AGILE 4.0 research project in a collaborative remote multidisciplinary approach. Results show that the engine retrofitting can be a profitable solution for both manufacturers and airliners. Conversely, the on-board-system electrification seems to be not convenient in a retrofitting process due to the high capital costs. Depending on the operative scenario, involved stakeholders can properly orient their decision on a retrofitting strategy.