Realistic assessments of the ecological status of benthic habitats, as requested by European directives such as the Water Framework Directive and the European Marine Strategy Framework Directive, require biotic indices capable of detecting anthropogenic impact without having preliminary knowledge of the occurring pressures. In this context, a new general-purpose biotic index (GPBI) based on the deviation of benthic macrofauna community composition and structure from a valid reference (i.e., good ecological status) is proposed. GPBI is based on the assumption that as a site becomes impacted by a pressure, the most sensitive species are the first to disappear, and that stronger impacts lead to more important losses. Thus, it explicitly uses the within-species loss of individuals in the tested station in comparison to one or several reference stations as the basis of ecological status assessment. In this study, GPBI is successfully used in four case studies considering the impact of diversified pressures on benthic fauna: (1) maerl extraction in the northern Bay of Biscay, (2–3) dredging and trawling in the North Sea, and (4) hypoxic events at the seafloor in the Gullmarfjord. Our results show that GPBI was able to efficiently detect the impact of the different physical disturbances as well as that of hypoxia and that it performs better than commonly used pressure-specific indices (M-AMBI and TDI). Signal detection theory was used to propose a sound good/moderate ecological quality status boundary, and recommendations for future monitoring are also provided based on the reported performance of GPBI.