This paper describes the development of a multi-phase/multi-criteria trajectory optimization framework that has been conceived to support the synthesis of green mission profiles that will allow aircraft to fly optimum flight paths with the lowest possible noise and emissions. The proposed multi-phase/multi-criteria framework is not only suitable to formulate trajectory optimization problems in which noise, emissions, or global warming effects can be simultaneously considered, but also provides the possibility to implement air traffic management constraints that apply to certain flight stages. A case study involving a trip from Amsterdam Airport Schiphol to Munich Franz Josef Strauss International Airport is presented to illustrate the synthesis of green trajectories and to demonstrate the potential for improving the environmental footprint. The optimization results bear out that optimizing with respect to noise can be very rewarding in terms of reducing the local noise impact, without significantly affecting the overall flight-economic performance.