Microbial control through alternative therapies, such as the amniotic membrane (AM) and antimicrobial photodynamic therapy (aPDT), has been gaining prominence with the advancement of bacterial resistance to conventional treatments. This study aimed to evaluate the antimicrobial effect of AM isolated and associated with aPDT using the PHTALOX® as a photosensitizer (PS) against Staphylococcus aureus and Pseudomonas aeruginosa biofilms. The groups studied were: C+; L; AM; AM+L; AM+PHTX; and AM+aPDT. The irradiation parameters were 660 nm, 50 J.cm−2, and 30 mW.cm−2. Two independent microbiological experiments were carried out in triplicate, and the results were analyzed by CFU/mL counting and a metabolic activity test, both statistically analyzed (p < 0.05). The integrity of the AM was verified after the treatments by a scanning electron microscope (SEM). The groups AM, AM+PHTX, and, mainly, AM+aPDT showed a statistical difference when compared to C+ regarding the decrease in CFU/mL and metabolic activity. SEM analysis showed significant morphological alterations in the AM+PHTX and AM+aPDT groups. The treatments with AM isolated or associated with PHTALOX® were adequate. The association had potentiated the biofilm effect, and the morphological differences presented by AM after treatment did not hinder its antimicrobial effect, encouraging its use in biofilm formation locals.