Soil organic carbon and nitrogen can be divided into labile and recalcitrant pools according to the time it takes to be cycled. The way in which carbon and nitrogen pools are cycled and distributed between labile and recalcitrant pools can directly relate to soil quality. This paper tested the hypothesis that labile and recalcitrant pools of carbon and nitrogen vary between agricultural soils with different species and fertilization management systems (nitrogen, phosphorus, and potassium need) under tropical conditions. This study aimed to examine the impact of land-uses on stocks and losses of carbon and nitrogen under tropical conditions. We explored labile (soil microbial biomass and labile carbon) and recalcitrant carbon pools (humin, humic acid, and fulvic acid) in forested and agricultural soils, defined as latosol (forest, fertilized pasture, and unfertilized pasture) and cambisol (forest, coast pasture, sugarcane, and silage corn). Forested soil was used as an appropriate use to soil conservation in tropical that presents levels adequate of carbon and nitrogen stocks and biological condition in soil. Results showed that pools of labile and recalcitrant carbon are different on soil layers and the use of soil. Forest use in cambisol and latosol promoted higher labile and recalcitrant pools of carbon and nitrogen due to the greater environmental stability without human intervention. On the other hand, human intervention occurred in fertilized pasture and coast pasture; however, both uses presented similar recalcitrant carbon and nitrogen pools when compared to forested soil on the soil surface due to fertilizer uses and the high volume of the grass root system. Overall, our findings reveal that under tropical conditions, agriculture and forested soil can present similar recalcitrant pools of carbon and nitrogen if agricultural soils are associated with the appropriate fertilizer management. Pasture with adequate fertilization management systems can be used as an alternative to recover degraded areas with low levels of recalcitrant carbon and nitrogen pools.