In this work, the catalytic aquathermolysis process of a Colombian heavy crude oil was studied. Reactivity tests were conducted in a microbatch reactor at 270 °C and saturation pressure of 5.5 MPa, during 66 h, using iron and molybdenum naphthenates in concentrations of 50−300 ppm as catalysts. The use of these catalysts reduced the gas yield from 1% to 4.2% w/w, the viscosity from 10% to 52.3% with iron naphthenate, and from 11.6% to 31.4% with molybdenum naphthenate. Crudes subjected to catalytic aquathermolysis increased their API gravity from 1.1 to 2.5 and 0.5 to 1.8 units, showing a significant decrease in complex fractions with boiling points above 340 °C and conversions in the order of 7% and 8% with respect to the precursors of molybdenum and iron naphthenates. Unlike other studies, the changes in the physical properties were correlated with changes in the chemical structure by ATR-FTIR spectroscopy. The average molecular parameters showed that the greatest differences with respect to the base crude oil were the length of the alkyl chains, the aromaticity, and the sulfurization. Results indicate different characteristics from the catalysts being studied, with iron naphthenate yielding better favorable effects in the change of the physicochemical properties of the improved crude oils. The experimental methodology proposed in this work indicates that the catalytic aquathermolysis process is a recovery method that allows for improving the properties of the crude oils, under reservoir conditions, due to the formation of products of smaller size and molecular weight.