This paper presents an optimisation framework to compute the altitude and speed profiles of a trajectory in the execution phase of the flight, such that the expected total cost (ETC) of the operation is minimised (i.e., modelling the expected cost of delay and fuel – including arrival uncertainties – at the arrival gate). This is achieved with a two-stage optimisation strategy: a trajectory optimiser that minimises a generalised direct operating cost function, for a given cost index; and an upper-level optimiser, which obtains the best cost index that minimises the ETC. Several case studies are presented for different departure delays, while considering the impact of two different weather forecast updates too: a region with relative high head-winds appearing half way across the flight; and a cold atmosphere scenario, with a tropopause altitude lower than standard conditions