Surface crystallography and polarity are shown to influence the detection probability of In, Ga, and N ions during atom probe tomography analysis of InxGa1−xN m-plane, c-plane, and (202¯1¯) quantum wells. A N deficit is observed in regions of the reconstruction generated from Ga-polar surfaces, and the probability of detecting group-III atoms is lower in InxGa1−xN quantum wells than in GaN barrier layers. Despite these artifacts, the detected In mole fraction is consistent throughout a given quantum well regardless of the crystal orientation of the quantum well or the evaporation surface from which the reconstruction was generated.