Industrial-scale mining of deep-sea polymetallic nodules will remove nodules in large areas and impact the physical integrity of the seafloor. However, environmental standards for seafloor integrity and studies of recovery from environmental impacts are still largely missing. Further we have only a poor understanding of the role of nodules in shaping benthic microbial diversity and element cycles. We revisited the deep-sea disturbance and recolonization experiment carried out with a towed plough harrow in 1989 in the Peru Basin nodule field within a circular area of approx. 3.5 km diameter (>4100 m water depth). In the experimental area, the 26 years old plough tracks were still visible and showed different types and levels of disturbance such as removal and compaction of surface sediments. Microbial communities and their diversity were studied in disturbance tracks and undisturbed sites and related to habitat integrity, remineralization rates, and carbon flow. Locally, microbial activity was reduced up to 4 times in the impacted areas. Microbial cell numbers were reduced by ~50% in fresh, and by <30% in the old tracks. Our data suggest that microbially-mediated biogeochemical functions need more than 50 years to return to undisturbed levels in the sediments. In areas with nodules (i.e., outside the disturbance tracks) microbial communities in the nodules themselves were studied. Nodule communities were distinct from sediments and showed a lower diversity and a higher proportion of sequences related to potential metal-cycling bacteria (i.e. Magnetospiraceae, Hyphomicrobiaceae), bacterial and archaeal nitrifiers (i.e. AqS1, unclassified Nitrosomonadaceae, Nitrosopumilus, Nitrospina, Nitrospira), as well as bacterial sequences typically found in ocean crust, hydrothermal deposits and sessile fauna. Our results confirm that nodules host specific microbial communities with potentially significant contributions to organic carbon remineralization and metal cycling. This study contributes to developing environmental standards for deep-sea mining and highlights the limits for maintaining and recovering ecological integrity and functions during large-scale nodule mining.