The plasma in future nuclear fusion reactors will be heated by neutral beam injectors (NBIs) and high frequency electromagnetic waves as well as fusion born alpha particles. Energetic particles (EPs), with energies up to two orders of magnitude larger than the thermal plasma, can trigger EP driven modes and induce harmful EP losses, reducing the plasma heating efficiency and the economical viability of the reactor. The present study is dedicated to analyze the Alfven Eigenmode (AE) activity in JET D–T discharges, the closest experiment to reactor-like operation performed until now. There, EP driven modes are induced by the combined effect of tangential NBIs and ion cyclotron resonance heating (ICRH) driven EP. Linear and nonlinear simulations are performed with the gyro-fluid FAR3d code to analyze the AE activity observed in the discharge 99896. The linear simulations reproduce the unstable n = 3 to 5 toroidal AEs (TAE) at the inner plasma region observed in the experiment, triggered by highly energetic passing deuterium populations injected by the tangential NBIs, further accelerated by the effect of the ICRH up to 1 MeV. In addition, fish-bones triggered by energetic trapped hydrogen induced by the ICRH are also reproduced. On the other hand, the alpha particles density is too small to destabilize AEs in the experiment. Nonetheless, increasing artificially the alpha density by one order of magnitude, an n = 1 beta induced AE can be destabilized in the inner plasma region. Nonlinear simulations indicate the generation of zonal structures during the AE/fish-bone saturation phase. TAE and fish-bones causes a rather weak increase of the passing D and trapped H EP (around 2%), respectively. Shear flows and zonal currents are generated during the saturation of TAE and fish-bones. Nonlinear simulations performed for D–T and pure deuterium thermal plasma indicate AE/fish-bone activity is weaker and shear flows are less intense in the pure deuterium case, trends consistent with the experimental observations that also indicates a deterioration of the thermal plasma confinement. Therefore, both numerical studies and experimental evidence indicate the generation of shear flows by AE/fish-bones could be connected with an improvement of the thermal plasma confinement.