A system and method for controlling an internal combustion engine for low emissions include an inner feedback control loop to control the engine fuel/air ratio with feedback provided by a first exhaust gas sensor and an outer feedback control loop that modifies a reference fuel/air ratio provided to the inner feedback control loop based on feedback signals provided by a second exhaust gas sensor positioned downstream relative to a portion of the catalyst and a third exhaust gas sensor positioned downstream relative to the second exhaust gas sensor. Catalyst gains are determined by modeling the catalyst as an integrator with an unknown gain and estimating the catalyst gain based on the exhaust gas sensors with the gain used to monitor catalyst performance and/or modify the engine fuel/air ratio.