In Amazonia, our knowledge of the trade-offs and possible thresholds in the relationships among social, economic and environmental parameters remains quite limited and hinders the design of sustainable socio-environmental systems. To fill this gap, we analyzed relationships among landscape metrics, socio-economic patterns, biodiversity and soil-based ecosystem services within a total of 51 farms located at 6 sites of the Colombian and Brazilian Amazon. Farms were representative of an initial set of 274 and they represented colonization ages from 10 to 80 years and a range of public policies found in the region. Cluster analysis separated farms in 7 types of production systems according to 5 main criteria (size of the farm, human capital, incomes, farm products and production intensity) selected from an initial set of 18 criteria. Biodiversity was summarized into a composite index Bd built with data from 8 different groups: trees, shrubs, grasses and forbs, birds, Saturnidae and Sphingidae moths, Drosophilidae, earthworms and ants. Provision of ecosystem services was quantified by a composite indicator of 6 sub-indicators of soil hydrological functions, C storage and chemical fertility. Increasing intensity of production systems was linked to a significant decrease of indicators of natural capital biodiversity (Bd) and soil based ecosystem services (Es) with 20% and 37.3% variance explained, respectively. No relationship was observed between production systems and an indicator of human wellbeing (Sb) based on a set of 5 criteria identified with the farmers. Findings indicate that early colonizers migrate when a certain level of development has been achieved (as a result of their activities) and are replaced by wealthier populations. An overall indicator of sustainability (Su) – that combines production efficiency (Ep), Sb, Bd and Es indices (ranging from 0.1–1.0) – decreases significantly with the landscape intensification (Li) with 18.7% variance directly explained