Aluminum gallium nitride [(Al,Ga)N] has gained significant attention in recent years due to its potential for highly efficient light emitters operating in the deep ultra-violet (UV) range (<280 nm). However, given that current devices exhibit extremely low efficiencies, understanding the fundamental properties of (Al,Ga)N-based systems is of key importance. Here, using a multi-scale simulation framework, we study the impact of alloy disorder on carrier transport, radiative and non-radiative recombination processes in a c-plane Al0.7Ga0.3N/Al0.8Ga0.2N quantum well embedded in a p–n junction. Our calculations reveal that alloy fluctuations can open “percolative” pathways that promote transport for the electrons and holes into the quantum well region. Such an effect is neglected in conventional and widely used transport simulations. Moreover, we find that the resulting increased carrier density and alloy induced carrier localization effects significantly increase non-radiative Auger–Meitner recombination in comparison to the radiative process. Thus, to suppress such non-radiative process and potentially related material degradation, a careful design (wider well, multi-quantum wells) of the active region is required to improve the efficiency of deep UV light emitters.