Polymetallic/ferro-manganese nodules (Mn-nodules) reach sizes of up to 10 cm in diameter and are abundantly found on the seabed. To date, the origin of Mn-nodules remains unclear, and both abiogenic and biogenic origins have been proposed. In search of evidence for a contribution of microbial processes to the formation of Mn-nodules, we analyzed those spherical nodules which contain a concentrically banded texture in their interior. The Mn-nodules were collected at a depth of 5,152 m from the Clarion-Clipperton Zone. Our high-resolution scanning electron microscopy analyses reveal first published evidence that endolithic microorganisms exist and are arranged in a highly organized manner on plane mineral surfaces within the nodules. These microorganisms are adorned on their surfaces with S-layers, which are indicative for bacteria. Moreover, the data suggest that these S-layers are the crystallization seeds for the mineralization process. We conclude that the mineral material of the Mn-nodule has a biogenic origin, and hope that these data will contribute to the development of biotechnological approaches to concentrate metals from seawater using bacteria in bioreactors.