The struggle over autonomy in farming is emblematic of the philosophical and practical tensions inherent in solving multi-scalar environmental issues. We explore the multiplicities of autonomy through comparative case studies of agricultural cooperation in England, Switzerland, New Zealand, and Brazil, which allow consideration of the implications of a range of approaches to managing farmed environments under different variations of neoliberalism. The original data emerge from separate projects examining aspects of cooperative autonomy in relation to the effects of the neoliberalisation of nature in agriculture. The comparative examination of autonomy and cooperation across distinct agri-food contexts highlights diversity in the social, ecological and economic outcomes of alternative forms of agri-environmental governance. This analysis provides a sobering corrective to both the over-romanticization of cooperation across global peasant movements and the over-romanticization of the individual entrepreneur in agro-industrial and family farming sectors. Our examination highlights the need for greater attention to the relationships between actors at and across different scales (the farm level, organizations and communities, the state, and industry) to understand how, in contrasting contexts of neoliberalisation, alternative conceptions of autonomy serve to mediate particular interventions and their material environmental consequences. A focus on actual autonomy, via the peasant principle and territorial cooperatives, creates an opening in theoretical and political dialogue to bridge concerns about farmers, livelihoods, and environmental outcomes.