Objective. To investigate the impact of the positioning of plane-parallel ionization chambers in proton beams on the calculation of the chamber-specific factor fQ and, hence, the beam quality correction factor . Approach. Monte Carlo simulations were performed to calculate the chamber-specific factor fQ in monoenergetic proton beams for six different plane-parallel ionization chambers while positioning the chambers with a) their reference point and b) their effective point of measurement accounting for the water equivalent thickness of the entrance window. Main results. For all ionization chamber models investigated in this study, the difference in fQ between both positioning approaches was larger for steeper dose gradients and bigger differences between the geometrical thickness and water-equivalent thickness of the entrance window. The largest effect was 1.2% for the IBA PPC-05 ionization chamber at an energy of 60 MeV. Significance. The positioning of plane-parallel ionization chambers in proton beams has a systematic impact on the fQ factor. This is especially of relevance for the factors presented in the recently updated TRS-398 code of practice (CoP) from IAEA. The background is that a positioning with the effective point of measurement is prescribed in TRS-398 CoP, however, all Monte Carlo derived data that have been employed for the update are based on a positioning of the ionization chambers with their reference point. Hence, the updated factors for plane-parallel ionization chambers in proton beams are subject to systematic errors that can be as large as 0.5%.