The present study aimed to fill the knowledge gap between the implications of intracellular and extracellular antibiotic resistance mechanisms may inflict on the inactivation pathways of the photo-Fenton process under mild conditions. It was thus designed as a cross-comparison of the effect of homogeneous and heterogeneous photo-Fenton (near-neutral pH, [Fe]=1 mg/L, and [H2O2]=10 mg/L) on seven strains of Staphylococcus aureus exhibiting different mechanisms of antibiotic resistance, or susceptibility. Additionally, variations in antibiotic tolerance (MIC test) and relative changes in the presence of antibiotic resistance genes were qualitatively monitored during treatment using PCR. The results suggest that resistance to antibiotics does not confer enhanced resistance to photo-Fenton, as it attained a 4-logU reduction within 50-100 min for all strains, regardless of resistance status. Strains that express intracellular resistance mechanisms do not pose a risk; however, strains that express external mechanisms for their defense against antibiotics occasionally interfere with the inactivation process. This phenomenon was mainly linked to the cell wall thickening of some of the externally resistant strains as compared to their susceptible homologues. Eventually, by conferring resistance to antibiotics, this cell wall alteration may reduce susceptibility to Fenton-related reagents by either reducing their intracellular diffusion or rendering cell walls less prone to leaching upon extracellular attacks. In addition, the photo-Fenton process either remained unchanged or lowered the antibiotic resistance threshold. Moreover, the homogeneous photo-Fenton system considerably lowered the detection of antibiotic resistance genes within 90 min with respect to hv, hv/H2O2, or heterogeneous photo-Fenton. In conclusion, the results suggest that the homogeneous photo-Fenton system could be an effective treatment for hindering the spread of antibiotic resistance, but treatment conditions should aim to maximize the degradation of ARG, as their concentration decreases more slowly than that of bacteria.