The runway usage of complex airports with multiple runways is currently prescribed by a preference list. The preference list mostly focuses on minimizing noise and it provides a more manageable flow for ATC. However, it does not consider the fuel burn or current demand of flights. This study presents a MILP scheduling model which optimizes for fuel burn and noise disturbance. This is done by a flexible allocation of flights to runways, therefore removing the use of a runway preference list. Furthermore, a separation method is developed to capture the dependencies within a complex runway system such that the model can be easily applied to every airport. The model is tested at Amsterdam Airport Schiphol and it is concluded that flexible scheduling has a positive impact on both objectives, resulting in more efficient airport operations and the possibility to expand operations within the current regulations.