This paper investigates the perceptions of a diversity of stakeholders supporting smallholders in the eastern Brazilian Amazon about ecosystem services and agricultural practices. Our results come from 30 semi-structured interviews with key stakeholders in two contrasting municipalities in this region (Paragominas and Irituia). We identified 17 different ecosystem services and 15 agricultural practices. Using a multidimensional scaling (MDS), we differentiated the stakeholders’ perceptions of co-production of ecosystem services. The most mentioned ecosystem services are food supply, regulation of water cycles, soil fertility and erosion prevention. Overall, there is a positive perception that agricultural practices are providing ecosystem services. Biodiversity-based practices are associated with the provision of a broad range of ecosystem services whereas mechanical-chemical practices are mainly linked to food supply. Use of fire, deforestation and use of chemical pesticides are perceived as having most negative effects on the provision of ecosystem services. The type of activity performed by the stakeholders and their municipality are the main factors influencing their perception of ecosystem services co-production. In conclusion, the concept of co-production of ecosystem services related to agroecosystems is relevant as local actors recognize a diversity of effects of agricultural practices on service provision.