Understanding Auger recombination in (In,Ga)N-based quantum wells is of central importance to unravelling the experimentally observed efficiency ‘droop’ in modern (In,Ga)N light emitting diodes (LEDs). While there have been conflicting results in the literature about the importance of non-radiative Auger recombination processes for the droop phenomenon, it has been discussed that alloy fluctuations strongly enhance the Auger rate. However, these studies were often focused on bulk systems, not quantum wells, which lie at the heart of (In,Ga)N-based LEDs. In this study, we present an atomistic analysis of the carrier density dependence of the Auger recombination coefficients in (In,Ga)N/GaN quantum wells. The model accounts for random alloy fluctuations, the connected carrier localisation effects, and carrier density dependent screening of the built-in polarisation fields. Our studies reveal that at low temperatures and low carrier densities the calculated Auger coefficients are strongly dependent on the alloy microstructure. However, at elevated temperatures and carrier densities, where the localised states are starting to be saturated, the different alloy configurations studied give (very) similar Auger coefficients. We find that over the range of carrier densities investigated, the contribution of the electron-electron–hole related Auger process is of secondary importance compared to the hole-hole-electron process. Overall, for higher temperatures and carrier densities, our calculated total Auger coefficients are in excess of 10−31 cm6 s−1 and may reach 10−30 cm6 s−1, which, based on current understanding in the literature, is sufficient to result in a significant efficiency droop. Thus, our results are indicative of Auger recombination being an important contributor to the efficiency droop in (In,Ga)N-based light emitters even without defect-assisted processes.