Multicriteria trajectory optimisation is expected to increase aviation safety, efficiency and environmental compatibility, although neither the theoretical calculation of such optimised trajectories nor their implementation into today’s already safe and efficient air traffic flow management reaches a satisfying level of fidelity. The calibration of the underlying objective functions leading to the virtually best available solution is complicated and hard to identify, since the participating stakeholders are very competitive. Furthermore, operational uncertainties hamper the robust identification of an optimised trajectory. These uncertainties may arise from severe weather conditions or operational changes in the airport management. In this study, the impact of multicriteria optimised free route trajectories on the air traffic flow management is analysed and compared with a validated reference scenario which consists of real flown trajectories during a peak hour of Europe’s complete air traffic in the upper airspace. Therefore, the TOolchain for Multicriteria Aircraft Trajectory Optimisation (TOMATO) is used for both the multicriteria optimisation of txrajectories and the calculation of the reference scenario. First, this paper gives evidence for the validity of the simulation environment TOMATO, by comparison of the integrated reference results with those of the commercial fast-time air traffic optimiser (AirTOp). Second, TOMATO is used for the multicriteria trajectory optimisation, the assessment of the trajectories and the calculation of their integrated impact on the air traffic flow management, which in turn is compared with the reference scenario. Thereby, significant differences between the reference scenario and the optimised scenario can be identified, especially considering the taskload due to frequent altitude changes and rescinded constraints given by waypoints in the reference scenario. The latter and the strong impact of wind direction and wind speed cause wide differences in the patterns of the lateral trajectories in the airspace with significant influence on the airspace capacity and controller’s taskload. With this study, the possibility of a successful 4D free route implementation into Europe’s upper airspace is proven even over central Europe during peak hours, when capacity constraints are already reaching their limits.