AlGaN/GaN-based pH sensors offer unique advantages of compact size, high sensitivity, and compatibility with lab-on-a-chip technologies. However, under reference electrode-free operation, researchers have reported two types of pH sensor response: linear (related to pH selectivity) and U-shaped (related to anion selectivity). To date, this distinct difference in behaviour has not been well explained and appropriate control experiments have not been conducted to elucidate the cause. In this paper, we compare the pH response of a reference electrode-free AlGaN/GaN device with and without a GaN capping layer. The results show that in the absence of a reference electrode, a linear response towards pH requires a GaN cap layer. This behaviour can be explained by the mitigation, when a GaN cap is used, of Coulombic interaction effects that occur between the electrolyte and surface states. Such interaction effects are only dominant when there is no reference electrode controlling the surface potential. There may also be secondary effects due to differences in the chemical surface chemistry of the oxides of aluminium and gallium. In the design of a reference electrode-free GaN transistor-based sensor technology, these factors must be taken into account.