Biomineralization is the process by which living organisms or organic matrices produced by them initiate and structure deposition of inorganic polymers/minerals. Deep-sea polymetallic nodules and crusts have recently been recognized as biominerals that are formed around bio-seeds; these deposits are of economic value. A detailed understanding of their formation will contribute to their sustainable exploitation in the future. Polymetallic nodules grow concentrically around discrete nuclei that have recently been described as bio-seeds formed from microorganisms, diatoms, or coccoliths. In the present study, polymetallic nodules from the Clarion-Clipperton Zone have been analyzed. It is described that the approximately 5-cm large polymetallic nodules are composed of micronodules (size of 100-450 μm) that aggregated to nests (2-3 mm). High-resolution scanning electron microscopy (HR-SEM) and high-resolution energy dispersive X-ray (HR-EDX) spectroscopic analyses revealed that the micronodules are composed of discrete layers of Mn and Fe. Imprints of microorganisms/microbe-like assemblies are found in the Mn-rich regions of the micronodules. HR-SEM/EDX analyses confirmed that these microorganisms are surrounded by a Mn-rich environment. These findings strongly suggest that those organisms acted as bio-seeds that allowed the deposition of Mn(IV) minerals which in turn helped Fe minerals to associate. Hence, these data support the concept that the growth of the polymetallic nodules starts as a biomineral and is completed by genuine mineralic depositions. It is expected that these data will contribute to the development of strategies for a sustainable exploitation of the polymetallic nodules.