BepiColombo is a mission to Mercury of the European Space Agency, in collaboration with the Japanese Space Agency, due to launch in July 2016. A spacecraft simulator is being developed by the European space industry for the European Space Operations Centre (ESOC) to support the operations. An Agile software methodology, based on iterative and incremental reviews and frequent prototype versions called sprints, has been applied for the first time in the development of a simulator at ESOC. This paper analyses the benefits and the impact of such dynamic process from the Flight Control Team perspective. It also presents the key innovations introduced in the BepiColombo simulator and in particular the use of a generic payload model that can be customized directly by the Flight Control Teamto simulate the behaviour of the spacecraft's payloads. How this generic approach to payload modelling can help to reduce the simulator development cost while providing more flexibility to the operations team is also the subject of this paper.