Biosurfactants and waterflooding have been widely reported thus far for enhancing oil production. Nevertheless, there is a lack of literature to explore enhanced oil recovered methods effects on its chemical composition. The aim of this work is to investigate the effects of a biosurfactant produced by Bacillus safensis and brine injection on the recovered petroleum composition, and their implications for geochemical interpretation. Original and oils recovered from displacement tests were analyzed by gas chromatography and ultra-high-resolution mass spectrometry, emphasizing saturated and aromatic biomarkers and basic and acidic polar compounds. Geochemical parameters based on some saturated compounds were subtly affected by the recovery methods, showing their reliable applicability in geochemical studies. Contrarily, parameters based on some aromatic compounds were more affected by biosurfactant flooding, mostly the low molecular weight compounds. Thus, these aromatic parameters should be applied with caution after such methods. The distribution of basic and acidic polar compounds can also be modified affecting the geochemical interpretation. In the case of the basic ones, the biosurfactant greatly influenced the N class species with favorable loss of lower aromaticity compounds. In addition to water solubilization, the compositional changes described in this study can be related to fractionation due to adsorption on reservoir rocks.