Magnetite is the most abundant magnetic iron mineral on the Earth’s surface. Its formation in natural ecosystems is mainly due to microbial activity. Microbially synthesized magnetite, commonly called “biogenic magnetite,” has many beneficial properties for a wide range of environmental and commercial applications. Its high surface reactivity facilitates interactions with (in)organic pollutants in anthropic and natural ecosystems, as well as with reagents in industrial catalysis. Due to its magnetic properties and good biocompatibility, biogenic magnetite is also well suited for biomedical applications such as cancer treatment or drug delivery. Biomineralization of magnetite offers an inexpensive and sustainable method for the production of this highly functional material. Moreover, this biomineralization process results in a biomolecule coating of the magnetite, making it highly amenable to further functionalization. This chapter reviews the application of biogenic magnetite across environmental, medical, and industrial settings. Existing challenges and future opportunities in these applications are also discussed.