The rehabilitation of coal mine sites in semi-arid environments is a step in combating desertification. A promising rehabilitation approach involves the development of anthropic soils that can support vegetation. However, reliable soil quality indicators are needed to evaluate long-term sustainability of rehabilitation strategies. In a coal mine area in northeastern Spain, two anthropic soils (0.5 m thick) were constructed by layering fine-textured coal residues at the bottom, topped with coarse overburden materials. Chemical fertility was enhanced using combinations of semi-liquid manure (25 or 60 mm) and straw (0 or 15 Mg ha-1), resulting in four treatments randomly distributed across both soil surfaces. Two abiotic indicators were selected for sustainability assessment: soil organic carbon (SOC) fractions and microstructure. Seven years after rehabilitation activities were completed, SOC fractions were analyzed. In addition, two years later, soil porosity and specific pore perimeter were also assessed in soil thin section images. The results indicated that the lower manure rate promoted more efficient SOC stabilization, evidenced by a 4-5-fold increase in specific pore perimeter at 0-5 cm depth, and lower fulvic acid content at 5-20 cm depth, compared with the higher manure rate. Micromorphological analysis proved to be a sensitive method for detecting early improvements in the physical quality of anthropic soils, highlighting the importance of adjusting manure rates for sustainable coal mine rehabilitation.