The integrated modelling of two plasma scenarios, hybrid and baseline, envisaged for the second operational phase (OP2) of the JT-60SA tokamak has been performed using the 1.5-dimensional JINTRAC suite of codes and the Bohm/gyro-Bohm (BgB) semi-empirical transport model. The decision to use the BgB model is driven not only by its widespread application in predicting scenarios for JET and JT-60U similar to those anticipated for JT-60SA, but also by its low computational cost. Two versions of the hybrid scenario—3.7 MA/2.28 T and 2.7 MA/1.70 T with MW—were optimized with respect to the reference METIS simulation to maintain a safety factor with a low magnetic shear region, and low shine-through losses. The results suggest that a high- () regime with a high non-inductive current fraction () could be achieved during the initial research phase at 2.7 MA/1.70 T and at a Greenwald density fraction . Hybrid-like q profiles are expected to be more easily obtained at higher Greenwald density fractions (0.6–0.8), while at lower densities, challenges such as hollow current density profiles and reversed q profiles were mitigated by adjusting the negative-neutral beam injection power and the injector configuration. The baseline scenario—4.6 MA/2.28 T with MW—demonstrated potential for high confinementperformance, achieving values of , , and MJ. A scan of the temperature pedestal height and its effect on plasma performance underscores the need to develop a physics-based model capable of accurately predicting the H-mode pedestal.