To develop a Monte Carlo (MC)-based and robust ion beam therapy optimization system that separates the optimization algorithm from the relative biological effectiveness (RBE) modeling. Robustly optimized dose distributions were calculated and compared across three ion therapy beams (proton, helium, carbon). The effect of different averaging techniques in calculating RBE in mixed beams was also investigated. Ion particles were transported in TOPAS MC. The microdosimetric-kinetic model (MKM) parameter, saturation corrected specific energy ([Formula: see text]), was calculated with a customized MKM implementation in TOPAS MC. Intensity modulated ion therapy robust optimization was performed by a quasi-Newton iterative method based on dose-volume objective function. The robust optimization took setup and range uncertainties into account. In the present work, the biological dose for each individual spot was calculated, and then summed together to calculate total biological dose. In other published works, radiosensitive parameters, such as [Formula: see text], were first averaged over all beam spots within a mixed-beam field, after which biological dose was calculated using the averaged radiosensitive parameters. The difference between the two mixed-beam biological dose calculations was quantified. Robust plans were achieved with the three particle types. The effect of averaging [Formula: see text] depended on particle type. The difference between biological doses calculated with individual [Formula: see text] and averaged [Formula: see text] may be greater than 3% for a carbon beam. MC based radiobiological and robust optimization was made flexible to incorporate dose-volume histogram constraints and to be independent of RBE models. Iterative optimization with RBE models was feasible. Evaluation of the RBE calculation for mixed beam could be necessary if better accuracy was demanded.