Increasing cultivation on acid soils of Colombia’s Eastern High Plains in the Orinoquia region require crop management strategies that balance commercial and environmental interests. Previous research showed the effects of land preparation and management on certain aspects of ecosystem services of these acid soils. This research aimed to comprehensively evaluate the impact of use and soil management in a native savanna Oxisol converted to five production systems gaining traction among local farmers: Annual crops rotation–sugarcane (ACR-S); Annual crops rotation-maize-soybean (ACR-MS); Sugarcane monocrop (SM); Rubber associated with Desmodium ovalifollium (R-Do) as a cover crop; Pasture Brachiaria decumbens - Annual crops rotation (PBd-ACR) and native savanna (NS) as a control. The experimental design consisted of conditioning the soil with two doses of dolomitic lime and incorporating three tillage methods over 5 years. A Principal Components Analysis (PCA) constructed indicators of ecosystem services (ES), such as fertility, water regulation, macroinvertebrate diversity, climate control related to greenhouse gas emissions (GHG) and carbon stock. The indicator values were adjusted between 0.10 and 1.0. Physicochemical variables with the greatest statistical weight were identified for components 1 and 2 each year. The fertility indicator of the native savanna for year one had a low range with a value of 0.11 compared to the other systems (p ≤ 0.05). During the years two, three, and four, soil fertility increased in the PBd-ACR (0.51) production system compared to the other systems. PBd-ACR generally improved water supply, although with lower indicator values than ACR-MS and R-Do. PBd-ACR show high biodiversity for edaphic macroinvertebrates compared to other systems. Field measurements detected methane emissions only in the SM system. Oxisols changed with the introduction of crops. The positive and negative tradeoffs of production systems and their agronomic practices should be considered in agricultural development of these acid soils.