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 understood. 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) in the NE Pacific. These small-scale disturbance experiments were performed 1 d 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 from the SE Pacific (Paul et al., 2018). We found that the upper 5–15 cm of the sediments was removed during various small-scale disturbance experiments in the different exploration contract areas. Transient transport-reaction modeling for the Polish and German contract areas reveals that the removal of the surface sediments is associated with the loss of the reactive labile total organic carbon (TOC) fraction. As a result, oxygen consumption rates decrease significantly after the removal of the surface sediments, and, consequently, oxygen penetrates up to 10-fold deeper into the sediments, inhibiting denitrification and Mn(IV) reduction. Our model results show that the return to steady-state geochemical conditions after the disturbance 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 reestablishment of bioturbation is essential, steady-state geochemical conditions are ultimately controlled by the delivery rate of organic matter to the seafloor. Hence, under current depositional conditions, new steady-state geochemical conditions in the sediments of the CCZ are reached only on a millennium scale even for these small-scale disturbances simulating deep-sea mining activities.