Deep-sea mining for manganese nodules appears to be an attractive option to supply the growing demand for metal resources. The technologies are advancing and the costs for deep-sea mining are dropping. The effect on the deep-sea ecosystems, in particular on microbial processes is hardly understood, making environmental management and monitoring efforts hard to focus. Long-term mining simulations can be used to assess the effects of deep-sea mining and the potential for recovery. We revisited a large-scale disturbance and recolonization (DISCOL) experimental area in the Peru Basin, 26 years after the disturbance and compared the disturbances with fresh tracks and reference areas. State of the art technologies and methods, such as, operations with a remotely operated vehicle (ROV), in situ flux measurements, estimation of biogeochemical parameters and activities, and investigation of microbial community structures via next generation sequencing, allowed the investigation of disturbances, related to deep-sea mining operations. During the disturbance simulations, surface sediment was removed, and suboxic subsurface layers were exposed. These deeper sediment layers had different microbial communities, lower amount of labile organic matter, less microbial biomass, and reduced activities. After 26 years, the organic matter did not rebuild, and cell numbers ,activities, and the assimilation efficiency stayed low. Only the community structure appeared to be recovered.