Dual fuel injection systems, like PFI+DI (port fuel injection + direct injection system) are being increasingly used in gasoline engine applications to increase the engine performance, fuel efficiency and reduce emissions. At a given engine operating condition, the air/fuel error is a function of the fraction of fuel injected by each of the fuel systems. If the fraction of fuel from each of the fuel system is changed at a given operating condition, the fuel system error will change as well making it challenging to learn the fuel system errors. This paper aims at describing the adaptive fueling control algorithm to estimate the fuel error contribution from each individual fuel system. Considering the fuel injection system slope errors to be the significant cause for air-fuel errors, a model structure was developed to calculate the fuel system adaptive correction factor as a function of changing fraction of fueling between the fuel systems. A recursive least squares estimation strategy was used to accurately estimate the individual fuel system correction factors and the same was implemented in real time on 3.5L GTDI engine. Algorithm was validated on different applications of dual fuel injection systems by inducing known amount of fueling errors on individual fuel systems (40% lean to 40% rich fueling faults). The results describe offline validation of the fueling correction model and the real time validation of the strategy. This real time estimation and control of the fueling errors from individual fuel system, significantly improves the air-fuel control of the dual fuel injection engines. This methodology additionally helps diagnose and separate each fuel system failure.