In Staphylococcus aureus infections in men eligible for doxycycline post-exposure prophylaxis (doxy-PEP), tetracycline non-susceptibility is more prevalent than in the overall population and is associated with resistance to trimethoprim-sulfamethoxazole and clindamycin. Doxy-PEP may select for S. aureus multi-drug resistance, underscoring the importance of surveillance.