Objective. While integration of variable relative biological effectiveness (RBE) has not reached full clinical implementation, the importance of having the ability to recalculate proton treatment plans in a flexible, dedicated Monte Carlo (MC) code cannot be understated . Here we provide a step-wise method for calibrating dose from a MC code to a treatment planning system (TPS), to obtain required parameters for calculating linear energy transfer (LET), variable RBE and in general enabling clinical realistic research studies beyond the capabilities of a TPS. Approach. Initially, Pristine Bragg peaks (PBP) were calculated in both the Eclipse TPS and the FLUKA MC code. A rearranged Bortfeld energy-range relation was applied to the initial energy of the beam to fine-tune the range of the MC code at 80% dose level distal to the PBP. The energy spread was adapted by dividing the TPS range by the MC range for dose level 80%–20% distal to the PBP. Density and relative proton stopping power were adjusted by comparing the TPS and MC for different Hounsfield units. To find the relationship of dose per primary particle from the MC to dose per monitor unit in the TPS, integration was applied to the area of the Bragg curve. The calibration was validated for spread-out Bragg peaks (SOBP) in water and patient treatment plans. Following the validation, variable RBE were calculated using established models. Main results. The PBPs ranges were within ± mm threshold, and a maximum of 5.5% difference for the SOBPs was observed. The patient validation showed excellent dose agreement between the TPS and MC, with the greatest differences for the lung tumor patient. Significance. A procedure for calibrating a MC code to a TPS was developed and validated. The procedure enables MC-based calculation of dose, LET, variable RBE, advanced (secondary) particle tracking and more from treatment plans.