Fungi contain species with a plethora of ways of adapting to life in nature. Consequently, they produce large amounts of diverse biomolecules that can be generated on a large scale and in an affordable manner. This makes fungi an attractive alternative for many biotechnological processes. Ascomycetes and basidiomycetes are the most commonly used fungi for synthesis of metal-containing nanoparticles (NPs). The advantages of NPs created by fungi include the use of non-toxic fungus-produced biochemicals, energy efficiency, ambient temperature, pressure conditions, and the ability to control and tune the crystallinity, shape, and size of the NPs. Furthermore, the presence of biomolecules might serve a dual function as agents in NP formation and also capping that can tailor the (bio)activity of subsequent NPs. This review summarizes and reviews the synthesis of different metal, metal oxide, metal sulfide, and other metal-based NPs mediated by reactive media derived from various species. The phyla ascomycetes and basidiomycetes are presented separately. Moreover, the practical application of NP mycosynthesis, particularly in the fields of biomedicine, catalysis, biosensing, mosquito control, and precision agriculture as nanofertilizers and nanopesticides, has been studied so far. Finally, an outlook is provided, and future recommendations are proposed with an emphasis on the areas where mycosynthesized NPs have greater potential than NPs synthesized using physicochemical approaches. A deeper investigation of the mechanisms of NP formation in fungi-based media is needed, as is a focus on the transfer of NP mycosynthesis from the laboratory to large-scale production and application.