The present study is dedicated to analyze the extensive fast ion (FI) induced perturbations in ion cyclotron resonance heating (ICRH) dominated plasmas in JET deuterium–tritium (D–T) discharges, the closest experiment to reactor-like operation. A set of nonlinear simulations are performed with the gyro-fluid FAR3d code to reproduce the FI induced activity and energetic particle (EP) transport observed in the discharge 99896 by multiple EP populations. Well validated simulations with JET D–T diagnostics show that Toroidal Alfvén eigenmodes (TAEs) and fish-bone are destabilized by ICRH accelerated passing D and trapped H ions, respectively. Multiple EP simulations show important nonlinear couplings between EP species, leading to a strong effect on the alpha particle confinement even in the alpha particles do not destabilize EP modes. Simulations including trapped H and alpha particles indicate fish-bones may induce alpha particle losses up to 3 % . The situation is different with respect to TAEs, which have a smaller impact on the alpha particle transport, leading to negligible losses. In addition, the generation of shear flows during the saturation phase of TAE and fish-bones is observed in the simulations. Shear flows induced by TAEs in the inner-middle plasma region are almost two times larger compared to the shear flows caused by the fish-bone in the inner plasma region. Shear flow generation by AE/fish-bones may have an important impact in the thermal plasma and alpha particle confinement of devices as ITER and JT60SA. Consequently, nonlinear effects in multiple EP populations must be considered in the analysis of EP transport. It is shown that this is a fundamental result that has to be considered to be properly evaluate fusion power in reactor relevant plasmas.