Understanding how the stored thermal energy scales with the main ion isotope, or mixtures of isotopes, in a tokamak is a key question for predicting the performance of future deuterium–tritium operations in ITER and fusion power plants. Although this remains an active area of research, a complete understanding has yet to be achieved. In this study, three JET H-mode discharges with matched engineering parameters are analysed to provide further experimental and analytical input into the investigation of mass scaling of the plasma turbulent transport. The discharges comprise one almost pure hydrogen, one mixed hydrogen–deuterium and one almost pure deuterium plasma. The analysis employs both linear gyrokinetic simulations and an integrated modelling framework. Particular attention is given to three mechanisms through which the mass of the main ion species is expected to influence the core thermal stored energy: (i) the boundary conditions set by the H-mode pedestal, especially in relation to stiff behaviour of temperature and density profiles; (ii) E × B shearing arising from neutral beam injection driven rotation; and (iii) the contribution of electron temperature gradient-modes to plasma transport. The results presented indicate that the pedestal and E × B shearing was key in explaining the increased thermal stored energy in the core in the analysed discharges.