Methods and systems are disclosed for fuel drift estimation and compensation using exhaust oxygen levels and fresh air flow measurements. An actual fueling to the engine cylinders is determined from the exhaust oxygen level and fresh air flow to the internal combustion engine. The actual fueling is compared to an expected fueling based on the fueling command provided to the internal combustion engine. The difference between the actual fueling and expected fueling is fuel drift error attributed to changes or drift in the fuel injection system and is used to correct or compensate future fueling commands for the fuel drift.