This study showed that cultivating mushrooms under Moso bamboo reorganizes the soil’s fungal community in ways that strengthen carbon retention and improve soil health over time. Across three species, soils saw increases in key carbon fractions like mineral-associated organic carbon during the first two years, alongside a shift from scattered fungal networks to more stable, aggregated structures linked to better carbon storage. Some species (like Morchella esculenta) boosted particulate organic carbon, while others had mixed early effects that improved once spent substrate was returned to the soil. Overall, the findings show that forest mushroom–based agroforestry can enhance soil carbon and fungal stability, making it a promising climate-smart practice for healthier forests and long-term carbon sequestration.