The thriving interest in harvesting deep-sea mineral resources, such as polymetallic nodules, calls for environmental impact studies, and ultimately, for regulations for environmental protection. Industrial-scale deep-sea mining of polymetallic nodules most likely has severe consequences for the natural environment. However, the effects of mining activities on deep-sea ecosystems, sediment geochemistry and element fluxes are still poorly conceived. Predicting the environmental impact is challenging due to the scarcity of environmental baseline studies as well as the lack of mining trials with industrial mining equipment in the deep sea. Thus, currently we have to rely on small-scale disturbances simulating deep-sea mining activities as a first-order approximation to study the expected impacts on the abyssal environment. Here, we investigate surface sediments in disturbance tracks of seven small-scale benthic impact experiments, which have been performed in four European contract areas for the exploration of polymetallic nodules in the Clarion-Clipperton Zone (CCZ). These small-scale disturbance experiments were performed 1 day to 37 years prior to our sampling program in the German, Polish, Belgian and French contract areas using different disturbance devices. We show that the depth distribution of solid-phase Mn in the upper 20 cm of the sediments in the CCZ provides a reliable tool for the determination of the disturbance depth, which has been proposed in a previous study (Paul et al., 2018). We found that the upper 5–15 cm of the sediments were removed during various small-scale disturbance experiments in the different exploration contract areas. Transient transport-reaction modelling for the Polish and German contract areas reveals that the removal of the surface sediments is associated with the loss of reactive labile organic carbon. As a result, oxygen consumption rates decrease significantly after the removal of the surface sediments, and consequently, oxygen penetrates up to tenfold deeper into the sediments inhibiting denitrification and Mn(IV) reduction. Our model results show that the post-disturbance geochemical re-equilibration is controlled by diffusion until the reactive labile TOC fraction in the surface sediments is partly re-established and the biogeochemical processes commence. While the re-establishment of bioturbation is essential, the geochemical re-equilibration of the sediments is ultimately controlled by the burial rates of organic matter. Hence, under current depositional conditions, the new geochemical equilibrium in the sediments of the CCZ is reached only on a millennia scale even for these small-scale disturbances simulating deep-sea mining activities.