Coping with complex landscape situations in the Anthropocene increasingly demands innovative governance practices that can be facilitated by investment in new epistemological and methodological approaches and capacities. This paper explores the use of a multimethodological research approach organized as a systemic co-inquiry to assist in the design of systemic governance for Agroextractivist Settlement Projects (PAEs) in the municipality of Abaetetuba, Pará, in the Brazilian Amazon. In the PAEs, the systemic co-inquiry was conducted alongside interested and influential stakeholders through the combined use of the Soft Systems Methodology and Strategic Options Development and Analysis problem structuring methods. The use of these methods and their tools allowed stakeholders to articulate major issues around the situation of concern, engaging in reflective practices about the opportunities of governing the PAEs systemically. By valuing stakeholder perspectives and participation in all phases of the research, the proposed multimethodology approach helped them express their views on the problem situation and allowed for their active engagement in the design of systemic governance of the PAEs. As a result of adopting a multimethodological approach, distinctive albeit coupled realms of governing are explored, a key issue when designing systemic governance practices of social-ecological systems such as the PAEs.