The influence of biodiversity and age of agroforestry systems (AFS) on the provision of ecosystem services, such as nutrient cycling, needs to be better understood to support management practices that promote such services. This study aimed to quantify and compare litter stock and the physical and chemical attributes of soil in four AFSs with different ages and arrangements to a secondary forest (FLO) in the Eastern Amazon. Litter stock did not differ among the AFSs, but the youngest AFS was lower (5.73 ± 1.04 Mg ha− 1) than in FLO (11.42 ± 2.44 Mg ha− 1). Similarities were found between FLO and the oldest AFS for most of the soil chemical attributes. The soil pH in AFSs was higher than in FLO in the surface layer, and the organic matter content of FLO did not differ from 2 and 51-year-old AFSs. The Al content and aluminum saturation of younger and 26 years-old AFSs were lower than in FLO. Particle density and total porosity did not differ among ecosystems, while soil density in the two younger AFSs was higher than in FLO. According to PCA results, variables such as organic matter, CECpH7, H + Al, Al content, and m % tended to be higher in FLO and oldest AFS. It was evident that the maturity and diversity of AFSs are relevant factors for Amazonian agroforests, as they offer positive impacts on ecosystem functionality, such as nutrient cycling and water retention.