Silvopastoral systems (SPS) are strategic in neutralizing greenhouse gases (GHG) emissions in livestock production systems, particularly in the tropics. This research assessed the mitigation potential of SPS on the carbon footprint (CFP) neutralizing in one integrated livestock farm of cow-calf and pig production system in the Colombian Amazon. Annual carbon accumulation rate (ACAR) in MgCO2e ha−1y−1, was evaluated on living above-ground biomass including trees and shrubs > 2 cm DBH and pasture, and leaf litter and below-ground biomass including coarse and fine roots, soil organic carbon 0–10 cm deep, and total ACAR adding up all components in live fences (LF), scattered trees (ST), fallows (FW), fodder bank (FB) and pastures (PT). The GHG emissions in MgCO2e ha−1y−1 were accounted in CO2 from liming, urea, fuel, electricity, and supplementation, CH4 from enteric methane, manure, and organic fertilization and N2O from urine and manure. The C balance was obtained from the differences between ACAR of SPS on farm and the CFP per surface. Mean total ACAR expressed in MgC ha−1y−1 were 9.0 ± 4.6 in FW, 7.0 ± 1.2 in LF, 5.5 ± 0.8 in ST, 4.2 ± 0.2 in FB and 2.9 ± 0.1 in PT. Mean CFP was 3.7 MgCO2e ha−1y−1, 5.3 MgCO2e Live Weight ha−1y−1, and 23.6 MgCO2e Live Weight Gain y−1. The CFP (area) can be neutralized with total ACAR value of 2.1 ha−1 for LF, 1.6 ha−1 for FW, 2.6 ha−1 for ST, 3.5 ha−1 for FB and 5.1 ha−1 for PT. The Silvopastoral systems have a higher potential for neutralizing GHG emissions than pasture-based scenario when considering the ACAR in above-ground biomass.