It is well recognized that commercial beef cattle production systems have a major impact on climate change, mainly due to the emission of enteric methane (CH4). The objective of this research was to evaluate if integrating animal + pasture + timber production in silvopastoral systems (SPS) would help neutralize the impact of enteric CH4 emission by facilitating carbon storage as soil organic carbon (SOC). This paper reports a study conducted in Brazil with a herd of 150 cows in 100 ha of Urochloa brizantha with Eucalyptus urograndis, on four tree configurations: SPS 1-clone GG-100 at 2 × 3 × 15 m spacing; SPS 2-clone i-144 at 2 × 3 × 15 m; SPS 3-clone GG-100 at 3 × 15 m; and SPS 4-clone i-144 at 3 × 15 m. Based on data collected through eight consecutive years, the gas balance was estimated. For all SPS treatments average, the carbon dioxide equivalent (CO2e) of additional C stock exceeded the emissions. Considering only C sequestration from trees, the average CO2e sequestration was − 26.27 Mg·CO2e ha−1, while the average emissions of CO2 e was 23.54 Mg·CO2e ha−1 for enteric CH4 + pasture + tree, giving a net balance of − 2.73 Mg·CO2e ha−1. The “loss” of CO2e analyzed was compensated by the soil C sequestration in long-lived SOC pools, enhancing the resilience of farming systems by increasing soil organic matter and soil fertility capacity, mitigating greenhouse gas emissions, therefore, providing benefits in livestock production and for environmental remediation.