Background Pathogenic strains of Staphylococcus aureus can cause several diseases including septicemia and endocarditis, in spite of being a commensal species of the human microbiota. The current drug resistance of S. aureus raises the need for new antimicrobials, and natural products represent a feasible source for prospection of such compounds, due to features including the diversity of structures and mechanisms of action. Here, we provide evidence of the antimicrobial activity of methanolic of Psidium guajava and Passiflora edulis pulps against planktonic cells and biofilms of clinical isolates of S. aureus. Results The extracts were effective against the strains in concentrations up to 7.81 and 250 μg/mL for planktonic cells and biofilms, respectively. Antagonistic interactions of the extracts to antimicrobial drugs were observed. The pulps caused no cytotoxic effects on BGM cells. GC-MS analysis found relevant molecules, and UPLC analysis suggested the presence of flavonoids. To the best of our knowledge, this is the first antibiofilm evidence of such extracts. Conclusion The extracts seem to be safe and effective enough for more studies aiming at exploring isolated antimicrobial molecules using in vivo models for the treatment of staphylococcal diseases.