Résumé : Next-generation proton therapy centres are evolving towards compact designs to reduce construction and decommissioning costs. These centres typically combine clinical treatments with research programs, leading to higher beam currents and longer irradiation times than in clinical conditions, thus producing a more significant number of secondary particles per unit volume and time. The activation level is expected to be higher, increasing the ambient dose and the amount of radioactive waste generated by the end of the centre lifetime. To address these issues, we propose a novel methodology that simulates all relevant processes, such as beam optics, secondary particle generation, and materials decay, for evaluating concrete shielding activation and related radiation protection quantities throughout a centre lifetime. Our approach combines Beam Delivery Simulation (BDSIM), a Geant4-based particle tracking code, and the inventory code and library database FISPACT-II. BDSIM allows a single model to simulate primary and secondary particle tracking in the beamline, its surroundings, and all particle-matter interactions and provides realistic secondary particle fluences to FISPACT-II, which is used to compute materials activation at any point in time by solving the rate equations. We apply this methodology to the shielding design of the ProtherWal proton therapy research centre in Belgium, which is validated against prior MCNPX simulations. Our results highlight the efficiency of the newly developed Low Activation Concrete (LAC) in limiting shielding activation. The activated concrete volumes amassed after 20 years of centre operation drop from about 109.5 m3 with the regular concrete to about 5.4 m3 with the LAC. The developed method is extensively exercised to study the sensitivity of the accelerator loss model on the activation results and to compute the activation of the magnetic beamline elements. A hybrid monitoring and simulation setup of the shielding activation is carefully designed and proposed for the ProtherWal centre. A setup of four removable cores to be placed at critical locations in the cyclotron vault is optimised to experimentally monitor the long-term activation and validate the beneficial impact of the LAC mix. Finally, to close the loop, an extension of the methodology is developed to simulate the decay radiation of activated concrete shielding. Our BDSIM/FISPACT-II methodology allows a single Monte Carlo model to be used throughout all design phases, from beamline optimisation and shielding design to activation studies. It also provides relevant quantities for radiation protection studies during the system lifetime.