The present study focused on the experimental evaluation of the effect of mineralogy in oil upgrading under two hybrid steam injection technologies. The tests were carried out in a batch reactor, using iron naphthenate as the catalyst and flue gas. The physical changes of the crude were evaluated by density and viscosity measurements, while the variations of the crude molecular structure were quantified using nuclear magnetic resonance (1H NMR) spectroscopy. The results showed that for the technique with catalyst, the scenario with the highest proportion of clay increased the API gravity by 27% and reduced the crude viscosity by 39%. The additional upgrading was the result of mineral presence with a contribution of 13% due to H2 production and the inhibition of polymerization. Additionally, the presence of the mineral phase with flue gas in the system reverses some of the subprocesses of the aquathermolysis reactions that favor the improvement of the crude. For this hybrid technique, the best scenario was achieved in the absence of the mineral phase with an increase of 10% in API gravity and a reduction of 41% in viscosity concerning the base crude as a product of the flue gas mechanisms. The changes in the physical properties can be correlated with the modifications in the chemical structure of the crude oil. These changes were a result of dealkylation, hydrogenation, and condensation reactions, evidenced by the variation of average molecular parameters, obtained by 1H NMR, such as the aromaticity factor and the number of substituted rings.