Demands on effective diagnosis and therapy, especially in the antibacterial field, are increasing. This study presents multifunctional Fe3O4@NaGdF4:Yb:Er-HMME (Fe@UCNP-HMME) nanoparticles for applications in bioimaging as well as photodynamic therapy (PDT)/sonodynamic therapy (SDT). We constructed a core-shell structure of Fe3O4 and upconversion nanoparticles (UCNPs) for T-2-weighted MRI and upconversion luminescence (UCL) imaging both in vitro and in vivo. Moreover, we modified the surface of the Fe@UCNPs with the photo/sonosensitizer hematoporphyrin monomethyl ether (HMME), which could be excited to produce O-1(2) for photo/sonodynamic antimicrobial chemotherapy (PACT). Furthermore, deep tissue penetration of UCL and ultrasound led to the temporal induction of cytotoxicity when applied to drug-resistant Gram(+) and Gram(-) bacteria, by which these pathogens were efficiently killed through damage of the cell wall structure. In summary, we developed a multifunctional Fe@UCNP-HMME-based platform for both dual-modality imaging and photo/sonodynamic antimicrobial chemotherapy, employing its complementary array of UCL, T2-MRI, and O-1(2) production properties to kill bacteria (100%) through PDT and SDT. Our experimental results verify the excellent potential of Fe@UCNP-HMME for applications in diagnosis and therapy.