OBJECTIVE The IAEA TRS-398 code of practice details the reference conditions for reference dosimetry of proton beams using ionization chambers and the required beam quality correction factors (kQ ). Pencil beam scanning (PBS) systems cannot approximate reference conditions using a single spot. However, dose distributions requested in TRS-398 can be reproduced with PBS using a combination of spots. This study aims to demonstrate, using Monte Carlo (MC) simulations, that kQ factors computed/measured for broad beams can be used with scanned beams for similar reference dose distributions with no additional significant uncertainty. METHODS We consider the Alfonso formalism13 usually employed for nonstandard photon beams. To approach reference conditions similar as IAEA TRS-398 and the associated dose distributions, PBS must combine many pencil beams with range or energy modulation and shaping techniques that differ from those used in passive systems (broad beams). In order to evaluate the impact of these differences on kQ factors, ionization chamber responses are computed with MC (Geant4 9.6) in three different proton beams, with their corresponding quality factors (Q), producing a 10 × 10 cm2 field with a flat dose distribution for (a) a dedicated scanned pencil beam (Qpbs ), (b) a hypothetical proton source (Qhyp ), and (c) a double-scattering beam (Qds ). The tested ionization chamber cavities are a 2 × 2 × 0.2 mm³ air cavity, a Roos-type ionization chamber, and a Farmer-type ionization chamber. CONCLUSIONS Ranges of Qpbs , Qhyp , and Qds are consistent within 0.4 mm. Flatnesses of dose distributions are better than 0.5%. Calculated kQpbs,Qhypfpbs,fref is 0.999 ± 0.002 for the air cavity and the Farmer-type ionization chamber and 1.001 ± 0.002 for the Roos-type ionization chamber. The quality correction factors kQpbs,Qdsfpbs,fref is 0.999 ± 0.002 for the Farmer-type and Roos-type ionization chambers and 1.001 ± 0.001 for the Roos-type ionization chamber. CONCLUSIONS The Alfonso formalism was applied to scanned proton beams. In our MC simulations, neither the difference in the beam profiles (scanned beam vs hypothetical beam) nor the different incident beam energies influenced significantly the beam correction factors. This suggests that ionization chamber quality correction factors in scanned or broad proton beams are indistinguishable within the calculation uncertainties provided dose distributions achieved by both modalities are similar and compliant with the TRS-398 reference conditions.