Abstract Deep-seabed polymetallic nodule mining can have multiple adverse effects on benthic communities, such as permanent loss of habitat by removal of nodules and habitat modification of sediments. One tool to manage biodiversity risks is the mitigation hierarchy, including avoidance, minimization of impacts, rehabilitation and/or restoration, and offset. We initiated long-term restoration experiments at sites in polymetallic nodule exploration contract areas in the Clarion-Clipperton Zone that were (i) cleared of nodules by a preprototype mining vehicle, (ii) disturbed by dredge or sledge, (iii) undisturbed, and (iv) naturally devoid of nodules. To accommodate for habitat loss, we deployed >2000 artificial ceramic nodules to study the possible effect of substrate provision on the recovery of biota and its impact on sediment biogeochemistry. Seventy-five nodules were recovered after eight weeks and had not been colonized by any sessile epifauna. All other nodules will remain on the seafloor for several years before recovery. Furthermore, to account for habitat modification of the top sediment layer, sediment in an epibenthic sledge track was loosened by a metal rake to test the feasibility of sediment decompaction to facilitate soft-sediment recovery. Analyses of granulometry and nutrients one month after sediment decompaction revealed that sand fractions are proportionally lower within the decompacted samples, whereas total organic carbon values are higher. Considering the slow natural recovery rates of deep-sea communities, these experiments represent the beginning of a ~30-year study during which we expect to gain insights into the nature and timing of the development of hard-substrate communities and the influence of nodules on the recovery of disturbed sediment communities. Results will help us understand adverse long-term effects of nodule removal, providing an evidence base for setting criteria for the definition of “serious harm” to the environment. Furthermore, accompanying research is needed to define a robust ecosystem baseline in order to effectively identify restoration success. Integr Environ Assess Manag 2022;18:682–696. © 2021 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). KEY POINTS Adverse effects on benthic communities as expected from deep-seabed polymetallic nodule mining call for the application of the mitigation hierarchy—including restoration measures once feasibility and positive effects have been proven. We initiated long-term restoration experiments at sites in polymetallic nodule exploration contract areas in the Clarion-Clipperton Zone that were (i) cleared of nodules by a preprototype mining vehicle, (ii) disturbed by dredge or sledge, (iii) undisturbed, and (iv) naturally devoid of nodules. We deployed >2000 artificial ceramic nodules to study the possible effect of substrate provision on recovery of biota and its impact on sediment biogeochemistry, and loosened sediment with a metal rake to test the feasibility of sediment decompaction to facilitate soft-sediment recovery. Due to expected slow recovery rates and the need for detailed characterization of baseline conditions, we expect to gain conclusive knowledge on long-term adverse effects of nodule removal and on the effectiveness of restoration measures in the next 30 years.