This paper assesses the contribution of secondary particles to pencil and passively scattered proton beams, in particular when considering the dose-averaged linear energy transfer (LET(d)) in biological treatment planning. Proton Monte Carlo simulations are performed in water phantoms and for two patients, considering all primary and secondary particles, including recoils from inelastic nuclear interactions. Our results show that secondary protons exhibit LET(d) values up to a factor 10 higher than those of the primary protons at the same depth. Thus, secondary protons have a significant impact on the LET(d). Their contribution increases the LET(d) by ∼50% along the central axis and even >200% in the penumbra. Furthermore, the LET maximum after the peak changes from 12 to 15 keV µm(-1) when adding secondary protons to the primary contribution. This is important when modeling LET(d) with analytical methods. The contribution of recoils (A > 3) is observed to be 1.2% in the entrance region considering a prostate case. The degree of biological damage inflicted by recoils remains hard to quantify, but is discussed on the basis of detailed energy spectra. The results highlight the role of secondary protons in LET-based radiobiological effectiveness calculations for proton therapy and when analyzing radiobiological experiments. Furthermore, the findings demonstrate the impact of inhomogeneities on the LET and the subtle changes between the LET distributions of passively scattered and actively scanned beams.