Participatory modelling is commonly applied in climate change adaptation research to integrate stakeholder knowledge, beliefs, values and norms into modelling processes. However, participation is not neutral, and current climate change adaptation research is tailored toward those with sufficient resources to adapt, as opposed to those most in need of adaptation. These are commonly marginalized stakeholder groups who remain on the social, economic, and political periphery, driving their vulnerability to climate change impacts. This paper presents the concept of autonomy in the context of multi-level governance for climate change adaptation before examining past participatory modelling approaches, illustrating the lack of application as an emancipatory tool for increasing the autonomy of marginalized stakeholder groups. Therefore, a list of ten necessary conditions are listed for conducting participatory modelling for increasing the autonomy of marginalized stakeholder groups, strengthening multilevel governance for climate change adaptation. These theoretical foundations are intended to guide public policy and increase the societal impact of participatory modelling.