Landscape dynamics result from forestry and farming practices, both of which are expected to have diverse impacts on ecosystem services (ES). In this study, we investigated this general statement for regulating and supporting services via an assessment of ecosystem functions: climate regulation via carbon sequestration in soil and plant biomass, water cycle and soil erosion regulation via water infiltration in soil, and support for primary production via soil chemical quality and water storage. We tested the hypothesis that patterns of land-cover composition and structure significantly alter ES metrics at two different scales. We surveyed 54 farms in two Amazonian regions of Brazil and Colombia and assessed land-cover composition and structure from remote sensing data (farm scale) from 1990 to 2007. Simple and well-established methods were used to characterize soil and vegetation from five points in each farm (plot scale). Most ES metrics were significantly correlated with land-use (plot scale) and land-cover (farm scale) classifications; however, spatial variability in inherent soil properties, alone or in interaction with land-use or land-cover changes, contributed greatly to variability in ES metrics. Carbon stock in above-ground plant biomass and water infiltration rate decreased from forest to pasture land covers, whereas soil chemical quality and plant-available water storage capacity increased. Land-cover classifications based on structure metrics explained significantly less ES metric variation than those based on composition metrics. Land-cover composition dynamics explained 45 % (P < 0.001) of ES metric variance, 15 % by itself and 30 % in interaction with inherent soil properties. This study describes how ES evolve with landscape changes, specifying the contribution of spatial variability in the physical environment and highlighting trade-offs and synergies among ES.