The acceleration of ecological crises has driven a growing body of thinking on sustainability transitions. Agroecology is being promoted as an approach that can address multiple crises in the food system while addressing climate change and contributing to the Sustainable Development Goals. Beyond the more technical definition as, “the ecology of food systems”, agroecology has a fundamentally political dimension. It is based on an aspiration towards autonomy or the agency of networks of producers and citizens to self-organize for sustainability and social justice. In this article, we use the multi-level perspective (MLP) to examine agroecology transformations. Although the MLP has been helpful in conceptualizing historic transitions, there is a need to better understand: (a) the role of and potential to self-organize in the context of power in the dominant regime, and (b) how to shift to bottom-up forms of governance—a weak point in the literature. Our review analyzes the enabling and disabling conditions that shape agroecology transformations and the ability of communities to self-organize. We develop the notion of ‘domains of transformation’ as overlapping and interconnected interfaces between agroecology and the incumbent dominant regime. We present six critical domains that are important in agroecological transformations: access to natural ecosystems; knowledge and culture; systems of exchange; networks; discourse; and gender and equity. The article focuses on the dynamics of power and governance, arguing that a shift from top down technocratic approaches to bottom up forms of governance based on community-self organization across these domains has the most potential for enabling transformation for sustainability and social justice.