In this review, we highlight new insights and place the molecular mechanisms of the biogenesis of nanomaterials such as silicified frustules, coccoliths, magnetosomes and bacterial nanowires in the context of the complex biology of a microbial cell. The silicified frustules are formed by diatoms, which are a widespread group of organisms found in the oceans, fresh water, soil and wet surfaces. They are especially important in the oceans, where it is estimated that they contribute to 45% of total primary ocean production. Coccolith is a collective term that designates all of the biomineralized, calcified scales produced by extant and extinct haptophytes (single-celled algae). The orientation of magnetotactic bacteria is based on the presence of unique organelles, magnetosomes, which are intracellular, membrane-enclosed, nanometre-sized crystals of magnetic iron minerals. The discovery of bacterial conductive structures, called nanowires, has fascinated scientists for almost a decade. Nanowires enable bacteria to transfer electrons over micrometer distances to extracellular electron acceptors such as insoluble metal oxides or electrodes. The possible applications of these extremely interesting nanomaterials in different areas of life is also considered.