Coffee agroforestry systems are increasingly promoted as sustainable land-use strategies to restore degraded tropical landscapes while supporting agricultural production and climate change mitigation. However, their ability to recover soil carbon pools relative to natural forest regeneration remains uncertain, particularly in tropical Afromontane ecosystems. We hypothesized that coffee agroforestry systems partially restore soil carbon dynamics but remain functionally distinct from soils in regenerating and mature forests. To test this, we evaluated soil organic carbon, carbon stocks, microbial biomass carbon and nitrogen, soil respiration, and labile carbon across five land-use types: fallow agricultural land, two-year-old and seven-year-old coffee agroforestry systems, regenerating forest, and mature forest fragments. Soil samples were collected at 0–15 cm and 15–30 cm depths and were analyzed using standard laboratory and statistical approaches. Soil organic carbon decreased with depth and was consistently lower in coffee agroforestry systems compared with forest and fallow sites. Carbon stocks were largely similar across land uses but were significantly higher in regenerating forest. Microbial biomass and soil respiration were reduced in older agroforestry systems, indicating lower biological activity. Labile carbon was highest in forest systems and positively related to total carbon stocks. These results demonstrate that while coffee agroforestry systems can maintain soil carbon levels, they do not fully restore soil carbon dynamics and microbial functioning compared with natural forest regeneration. This study provides new insights into the role of agroforestry in soil carbon recovery and highlights the need to integrate agroforestry with forest restoration strategies to enhance soil health, ecosystem resilience, and climate change mitigation in tropical landscapes.