This study unites physicochemical indicators of aboveground vegetation, litter layer and topsoil (0–20 cm) in contrasting vegetation types commonly found in the eastern Amazonia. We compare three agroforestry systems (enriched fallows, homegardens and commercial plantations) with three spontaneous forest types (young and old secondary forests and mature rainforests) via one-way ANOVA, linear and non-linear regressions and multivariate analyses. Agroforests had significantly lower understory biomass when compared with young secondary forest. Commercial plantation agroforests had higher topsoil pH and Ca-contents and homegardens had higher K-contents and P-availability hotspots, as revealed by their higher variance and single very high values. Agroforests and spontaneous forests were similar in their litter biomass (both leaves and twigs) and C:N ratio, and in soil organic matter and P contents. The overstory negatively impacted the understory (r2 = 0.20, p < 0.05) and the understory correlated significantly with the litter layer (r2 = 0.11, p < 0.07). By contrast, there were no direct relationships between overstory and the litter layer, pointing to a major discontinuity between vegetation and topsoil. Principal component analysis depicted a successional sequence of systems, with homegardens closest to mature rainforests. According to co-inertia analysis, plant biomass was more strongly related to topsoil in spontaneous forests than in agroforests. Altogether, agroforests were similar to mature rainforests in a wide range of variables of the vegetation, litter and topsoil, and co-inertia analysis indicated that agroforestry management can alter this continuum. Our results point to an outstanding position of homegardens in the study region, with higher aboveground biomass and elevated nutrient availability which may have been caused by the traditional sweep-and-burn low-intensity fire regime prevalent throughout Amazonia and beyond.