There are describes methods and systems for operating an engine coupled to a fuel system having a fuel manifold configured to supply fuel to a combustor of the engine. The method comprises receiving a gaseous fuel flow request indicative of a change in demand for gaseous fuel to the engine; applying a fuel loss bias to the gaseous fuel flow request to obtain a biased fuel flow request, the fuel loss bias associated with a change in mass flow rate of the gaseous fuel from the fuel manifold to the combustor in response to the change in demand; and causing the gaseous fuel to flow into the combustor in accordance with the biased fuel flow request.