A method and system for controlling fuel delivery to an individual cylinder of an internal combustion engine during engine cranking compensates for fuel transport dynamics and the actual fuel injected into the cylinder. A plurality of engine parameters are sensed, including engine temperature, inducted air mass per cylinder and number of engine intake events since cranking. A temperature of the engine stored at key-off is determined. A new puddle mass estimate for the cylinder is determined based on the decay ratio of the new puddle mass estimate to the prior puddle mass estimate stored before key-off utilizing the temperature of the engine stored at key-off. A desired fuel mass to be injected into the cylinder is then determined based on the new puddle mass estimate and the plurality of engine parameters.