Objective To benchmark Monte Carlo codes FLUKA and GATE/Geant4 regarding the beam quality correction factors of ionization chambers for monoenergetic carbon-ion beams against experimental results by Holm et al (2022 Phys. Med. Biol. 67 49401). Approach Monte Carlo codes FLUKA and GATE/Geant4 were used to simulate the beam quality correction factor kQ for one plane-parallel (PTW 34001) and two cylindrical ionization chambers (PTW 30013 and IBA FC65-G) using two monoenergetic carbon-ion beams and an energy modulated beam in accordance with Holm et al (2022 Phys. Med. Biol. 67 49401). Additionally, chamber-specific factor fQ and perturbation factor pQ were calculated. Differences between Geant4 reference physics lists were investigated by comparing simulated depth dose distributions, fQ, and pQ values for 429 MeV u−1. Main results Simulated kQ factors were found to differ from experimentally determined kQ factors of Holm et al (2022 Phys. Med. Biol. 67 49401) by 2.5% for cylindrical chambers, whereas the plane-parallel chamber showed larger deviations of 3.1/2.6% (GATE/FLUKA), exceeding the simulation uncertainty of 1.7%. fQ and pQ factors simulated using different Geant4 physics lists were comparable within the Type-A uncertainty of 0.2%. Nevertheless, the depth dose curves for physics lists using the INCL++ model showed an increase in dose at all depths except for the fragmentation tail. Differences in fQ factors between Monte Carlo codes FLUKA and GATE of up to 1.8% have been observed. Significance More investigations are needed to understand the cause of the observed deviations between experimental results and Monte Carlo calculations of beam quality correction factor kQ. No statistically significant differences are observed between investigated Geant4 physics lists for fQ, kQ, and pQ simulations. Notably, differences between Monte Carlo codes FLUKA and GATE are one of the main sources that limit the current simulation uncertainty.