Miscanthus, a C₄ perennial rhizomatous grass, is a low-input energy crop suitable for marginal land, which cultivation can improve soil quality and promote soil organic carbon (SOC) sequestration. In this study, four promising Miscanthus hybrids were chosen to evaluate their short-term potential, in six European marginal sites, to sequester SOC and improve physical, chemical, and biological soil quality in topsoil. Overall, no differences among Miscanthus hybrids were detected in terms of impacts on soil quality and SOC sequestration. SOC sequestration rate after 4 years was of +0.4 Mg C ha⁻¹ year⁻¹, but land-use transition from former cropland or grassland showed contrasting SOC sequestration trajectories. In unfertilized marginal lands, cultivation of high-yielding Miscanthus genotypes caused a depletion of K (−216 kg ha⁻¹ year⁻¹), followed by Ca (−56 kg ha⁻¹ year⁻¹), Mg (−102 kg ha⁻¹ year⁻¹) and to a lesser extent of N. On the contrary, the biological turnover of organic matter increased the available P content (+164 kg P₂O₅ ha⁻¹ year⁻¹). SOC content was identified as the main driver of changes in biological soil quality. High input of labile plant C stimulated an increment of microbial biomass and enzymatic activity. Here, a novel approach was applied to estimate C input to soil from different Miscanthus organs. Despite the high estimated plant C input to soil (0.98 Mg C ha⁻¹ year⁻¹), with significant differences among sites and Miscanthus hybrids, it was not identified as a driver of SOC sequestration. On the contrary, initial SOC and nutrients (N, P) content, as well as their elemental stoichiometric ratios with C, were the key factors controlling SOC dynamics. Introducing Miscanthus on marginal lands impacts positively soil biological quality over the short term, but targeted fertilization plans are needed to secure crop yield over the long term as well as the C sink capacity of this perennial cropping system.