An engine control system and method includes sensing the quality of fuel in the engine relative to emissions, by for example sensing the level of an emission related constituent, such as sulfur. A fuel quality sensor detects a fuel quality of a fuel, such as the sulfur level the fuel, and provides a signal in response to the fuel quality. The engine control system also includes a navigation device to determine whether an engine is located in a regulated or non-regulated region. The engine control system receives the signal and controls engine operation by, for example, enabling or disabling one or more engine algorithms to improve performance of the engine based on the fuel quality signal or, in other embodiments, the combination of the fuel quality and the location of the engine.