Nanotechnology plays a big part in our modern daily lives, ranging from the biomedical sector to the energy sector. There are different physicochemical and biological methods to synthesise nanoparticles towards multiple applications. Biogenic production of nanoparticles through the utilisation of microorganisms provides great advantages over other techniques and is increasingly being explored. This review examines the process of the biogenic synthesis of nanoparticles mediated by microorganisms such as bacteria, fungi and algae, and their applications. Microorganisms offer a disparate environment for nanoparticle synthesis. Optimum production and minimum time to obtain the desired size and shape, to improve the stability of nanoparticles and to optimise specific microorganisms for specific applications are the challenges to address, however. Numerous applications of biogenic nanoparticles in medicine, environment, drug delivery and biochemical sensors are discussed.