After more than 20 years, mining of mineral resources, such as polymetallic nodules and massive sulfides, in the deep sea is back on the agenda of many countries and companies in their search for high-tech raw metals. In this course, the past 10 years have seen an immense increase of exploration licences issued by the International Seabed Authority (ISA), which organizes and controls activities at the ocean floor beyond national jurisdiction, generally termed the "area". The seven pilot investors are renewing their exploration licences for another five years, after which they will need to apply for an exploitation licence (or lose their contracted claim). Thus, ISA is currently developing the regulatory framework for the exploitation of seafloor mineral resources, which includes legislation to "ensure effective protection of the marine environment from harmful effects" according to UNCLOS article 145. In order to support decision-making for ISA's regulations, several benthic impact experiments were conducted more than 20 years ago. However, the impacts have only been studied over the following 5–7 years. Until now, no information has been available for the expected longer-term impacts induced by mining operations, i.e. in case of nodule mining the removal of the surface sediments and dispersal of the suspended particle plume and subsequent seafloor blanketing. Therefore, in 2015 the European project MiningImpact, funded through the Joint Programming Initiative Healthy Seas and Oceans (JPIO), revisited several impact scars at the seafloor in the nodule exploration licence areas of the Clarion–Clipperton Fracture Zone (CCZ) as well as the benthic impact experiment DISCOL (DIsturbance and reCOLonization) in the Peru Basin. Our scientific study provides the first results of environmental consequences on the deep-sea ecosystem that prevail for up to 40 years after a disturbance was created. Also, the impacted areas vary in size from single 1–2 nm long dredge or sled tracks to the 78 criss-crossing, 4 m wide plough harrow marks in the 11 km² large DISCOL experimental area. This special issue presents the scientific results of the biological, biogeochemical, geological, and oceanographic investigations carried out in the MiningImpact project (consisting of 25 institutes from 11 European countries) that is used to provide recommendations for the exploitation mining code of ISA (e.g. improved methods for the management and monitoring of mining operations) and to improve our understanding of the ecological functions of the deep seafloor.