The impact of substituting forests for smallholder agricultural production systems on soil carbon (C) stocks is not well understood in Brazilian Amazonia. Most surveys of soil C stocks are restricted to the top 30 cm of soil and do not include measurements of litter and root stocks. Here, we quantify the stocks of C in soil (0–100 cm depth), aboveground litter and coarse roots of traditional (slash‐and‐burn) and alternative (Schizolobium amazonicum‐planted forest and silvopastoral system) smallholder agricultural systems, which were compared with a reference area (forest regrowth) in the eastern Amazonia. The soil C stocks in the 0–100 cm layer were larger in the forest regrowth treatment (156.8 ± 15.5 Mg/ha) than in the other treatments (S. amazonicum = 85.3 ± 6.5, silvopastoral = 108.0 ± 4.4 Mg/ha) but did not differ from the soil C stock in the slash‐and‐burn treatment (127.2 ± 6.1 Mg/ha). The soil C stocks at the 0–30 cm layer, which represented 33–50% of the total C of the 0–100 cm layer, did not differ among the treatments. The litter C stocks were ranked in the following order: silvopastoral > forest regrowth > S. amazonicum > slash‐and‐burn. The forest regrowth treatment had a greater coarse root C stock (0.84 ± 0.10 Mg/ha) than the other treatments (silvopastoral = 0.28 ± 0.03, S. amazonicum = 0.18 ± 0.03, slash‐and‐burn = 0.27 ± 0.04 Mg/ha). Soil, litter and root C stocks were negatively impacted by the conversion of forest regrowth to cultivation systems.