Swidden smallholders are among the most vulnerable groups to climate change. Many efforts have focused on incentivizing their transition to agroforestry, often with limited results. Such transitions, embedded in complex socio-environmental changes, generate uncertainties, often ignored in the science-policy interface. In this paper, we examine dispersed disciplinary developments in decision-making under uncertainty, apply the insights to a case study, and discuss results in the context of prevalent knowledge production assumptions and incentivized livelihood transitions policies. We use interview data from three communities in the Mexican Maya region to create aggregated mental models of smallholders who adopted agroforestry, and those who continue to practice traditional swidden agriculture. The mental models depict perceived causal connections—including uncertain or delayed—between hazards, causes, consequences and responses. Our results show substantial differences in mental models driven by length of explanatory pathways, attribution of hazards and portfolios of responses, suggesting that agroforesters were more prone to proactive behavior and/or more responsive to outside discourses. Agroforestry is effective in reducing some uncertainties in its bundled approach, but new uncertainties for which smallholders have no prior experience arise. Contrastingly, recurrent themes point to lower self-efficacy in swidden smallholders, which may help explain non-adoption. We caution that not recognizing differences in mental models among potential beneficiaries of incentivized interventions may inadvertently exacerbate inequalities, while unaddressed uncertainties may lead to future disadoption. As a scientific tool, mental model mapping can inform the design of adaptation measures by identifying new knowledge and conflicting rationales, and segmenting strategies for potential (non)adopters.