Agroforestry systems have been promoted as a solution to address trade-offs between environmental conservation efforts and the need for increased agricultural productivity on smallholder farms in Brazil. However, the impact of land use change from degraded pasture to agroforestry on soil properties remains unclear. The objectives of this research were to: (1) assess soil chemical, physical and biological properties across distinct land uses (degraded pasture, agroforestry and secondary forest); and (2) understand relationships between litter quality, soil organic matter (SOM) and key soil quality parameters in the Brazilian Atlantic Rainforest. Soils, macroinvertebrates and litter were collected in April and September of 2018 under five land uses, including: three types of agroforestry systems, a degraded pasture and a secondary forest in Sapucaia, Rio de Janeiro, Brazil. Our results showed that soil properties clearly separated the three agroforestry systems plots (AS1, AS2, AS3) from the forest and pasture plots. Moreover, litter quality and SOM likely influence multiple biological and physiochemical soil properties under agroforestry systems and secondary forest. Our findings suggest that agroforestry systems can help support soil biological, chemical and physical properties and that the litter quality may be an important driver of their effects and potential contributions to soil restoration in the region.