After the successful Global Coverage of the Digital Elevation Model, the TanDEM-X Science phase was initiated in September of 2014, dedicated to the demonstration of innovative techniques and experiments. The TanDEM-X Science phase had a large impact on the TerraSAR-X/TanDEM-X Mission Planning System. The two main challenges were the formation flying changes and the activation of a new acquisition mode, the so called Dual Receive Antenna (DRA) acquisition mode. This paper describes all actions and quantitative analyses performed in order to achieve the twofold target of the Mission Planning System: a) support the new TanDEM-X mission’s requirements, while b) proceed seamlessly with the TerraSAR-X mission fulfilling both its scientific and commercial demands. Regarding the first objective, several system reconfigurations are presented which were executed either due to the new flying formations or due to enabling the new DRA acquisition mode. In parallel, various analyses are included for the ground station visibilities of each formation and the distribution of the S- and X-Band contacts. For the second objective, it is presented how, via new concepts and mechanisms, it was possible to continue the TerraSAR-X mission undisturbed. Statistical analyses depict their successful integration and performance in the operational system. As a heritage of the TanDEM-X Science phase, the statistical analyses have become a very useful tool for the daily operations of both satellites and missions.