This study investigates the interactions of primary and secondary bile acids (cholic acid (CA), chenodeoxycholic acid (CDCA), ursodeoxycholic acid (UDCA), and lithocholic acid (LCA)) with isolated rat liver mitochondria, focusing on their uncoupling activity, detergent effects, and antioxidant properties. Using a recently developed methodological approach based on quantifying the effective distribution coefficient ( \(\:{E}_{MW}\) ), we precisely assessed the partitioning of bile acids between the mitochondrial and aqueous phases. Our results demonstrate that the uncoupling potency rank order was LCA > CDCA > CA, which strongly correlated with their lipophilicity. In contrast, UDCA, which possesses hydroxyl groups on the hydrophobic β-surface, exhibited significantly lower uncoupling activity. At concentrations inducing mild uncoupling (stimulating state 4 respiration by 70–75%), all bile acids significantly reduced the ADP/O ratio and respiratory control ratio without inhibiting the electron transport chain, confirming their protonophoric mechanism. Furthermore, we quantitatively showed that bile acids, in contrast to palmitic acid, exert a mild detergent effect, as evidenced by a increase in NADH-stimulated respiration, with UDCA and CA having the most pronounced effect. Crucially, at these uncoupling concentrations, all bile acids consistently suppressed mitochondrial H2O2 generation by 30–40%, revealing their antioxidant potential. These findings provide quantitative insights into the structure-dependent dual roles of bile acids in modulating mitochondrial function.