To improve the penumbra of low‐energy beams used in spot‐scanning proton therapy, various collimation systems have been proposed and used in clinics. In this paper, focused on patient‐specific brass collimators, the collimator‐scattered protons' physical and biological effects were investigated. The Geant4 Monte Carlo code was used to model the collimators mounted on the scanning nozzle of the Hokkaido University Hospital. A systematic survey was performed in water phantom with various‐sized rectangular targets; range (5–20 cm), spread‐out Bragg peak (SOBP) (5–10 cm), and field size (2 × 2–16 × 16 cm2). It revealed that both the range and SOBP dependences of the physical dose increase had similar trends to passive scattering methods, that is, it increased largely with the range and slightly with the SOBP. The physical impact was maximized at the surface (3%–22% for the tested geometries) and decreased with depth. In contrast, the field size (FS) dependence differed from that observed in passive scattering: the increase was high for both small and large FSs. This may be attributed to the different phase‐space shapes at the target boundary between the two dose delivery methods. Next, the biological impact was estimated based on the increase in dose‐averaged linear energy transfer (LETd) and relative biological effectiveness (RBE). The LETd of the collimator‐scattered protons were several keV/μm higher than that of unscattered ones; however, since this large increase was observed only at the positions receiving a small scattered dose, the overall LETd increase was negligible. As a consequence, the RBE increase did not exceed 0.05. Finally, the effects on patient geometries were estimated by testing two patient plans, and a negligible RBE increase (0.9% at most in the critical organs at surface) was observed in both cases. Therefore, the impact of collimator‐scattered protons is almost entirely attributed to the physical dose increase, while the RBE increase is negligible.