OBJECTIVE Beam quality correction factors provided in current codes of practice for proton beams are approximated using the water-to-air mass stopping power ratio and by assuming the proton beam quality related perturbation correction factors to be unity. The aim of this work is to use Monte Carlo simulations to calculate energy dependent beam quality and perturbation correction factors for a set of nine ionization chambers in proton beams. METHODS The Monte Carlo code EGSnrc was used to determine the ratio of the absorbed dose to water and the absorbed dose to the sensitive air volume of ionization chambers related to the reference photon beam quality (60 Co). For proton beams, the quantity was simulated with GATE/Geant4 for five monoenergetic beam energies between 70 MeV and 250 MeV. The perturbation correction factors for the air cavity, chamber wall, chamber stem, central electrode, and displacement effect in proton radiation were investigated separately. Additionally, the correction factors of cylindrical chambers were investigated with and without consideration of the effective point of measurement. RESULTS The perturbation factors were shown to deviate from unity for the investigated chambers, contradicting the assumptions made in dosimetry protocols. The beam quality correction factors for both plane-parallel and cylindrical chambers positioned with the effective point of measurement at the measurement depth were constant within 0.8%. An increase of the beam quality correction factors determined for cylindrical ionization chambers placed with their reference point at the measurement depth with decreasing energy is attributed to the displacement perturbation correction factors , which were up to 1.045 ± 0.1% for the lowest energy and 1.005 ± 0.1% for the highest energy investigated. Besides , the largest perturbation was found for the chamber wall where the smallest determined was 0.981 ± 0.3%. CONCLUSIONS Beam quality correction factors applied in dosimetry with cylindrical chambers in monoenergetic proton beams strongly depend on the positioning method used. We found perturbation correction factors different from unity. Consequently, the approximation of ionization chamber perturbations in proton beams by the respective water-to-air mass stopping power ratio shall be revised.