Eucalyptus plantations play an important role in capturing and storing atmospheric carbon, mitigating global climate change. Forest management policies encouraging integrated livestock-forestry systems require quantitative estimates of temporal and spatial patterns of carbon storage for these agricultural systems. This study quantified the effects of eucalyptus management and arrangement on carbon stock dynamics in integrated livestock-forestry (ILF) systems versus monoculture eucalyptus plantings. Arrangement and management resulted in equal storage of carbon in both monoculture and ILF systems (34.7 kg per tree). Both factors are important to better understand how forest species in integrated systems stock carbon and how this can compensate for other agricultural system components, such as cattle. The extent to which ILF systems offset beef cattle (Nellore) emissions was determined by estimating changes in carbon stock over time for Eucalyptus urophylla × E. grandis, clone H13, under three scenarios (S) of wood use. These scenarios were (S1) tree growth without thinning, (S2) trees used for biomass energy without thinning, and (S3) 50% of trees used for biomass energy at five years old and 50% of trees used for both timber and energy after eight years, considering the full life cycle of eucalyptus. The S1 and S3 systems can stock 510 and 358 metric tons (t) of CO2 ha−1, respectively, while S2 emits 112 t CO2 ha−1 of biogenic carbon.