This study provides experimental evidence of charged interface states limited scattering in III-nitride heterostructures. Temperature-dependent Hall measurements and temperature-dependent ID–VG measurements indicate a significant influence of the charged interface states on the electron mobility in different AlGaN/GaN heterostructures where the characteristic of the interface is controlled by modulating the growth conditions. Charged interface states at the AlGaN/GaN heterointerface lead to electron scattering as the distance between the centroid of the two-dimensional electron gas and the interface decreases with increasing electron density. It is observed that a component of experimental Hall mobility, which ranges between 9.2 × 103 and 3.4 × 104 cm2/V s among the three samples, obtained after adding all the scattering events using Matthiessen's rule cannot be explained completely by considering all the conventional scattering mechanisms such as phonon–phonon scattering, interface roughness scattering, and dislocation density scattering. An in-depth analysis reveals a significant scattering of channel electrons by the charged states at the GaN/AlN/AlGaN interface. Furthermore, the estimated interface states from the temperature-dependent subthreshold slopes conducted on the fabricated high electron mobility transistors are in good agreement with the charged interface states extracted from the temperature-dependent Hall measurements. A good understanding on this new scattering mechanism in the GaN heterostructure may help in designing high-performance III-nitride devices in the future.