This paper focuses on how the use of Community OR (COR), specifically Systems Thinking (ST) and the Viable System Model (VSM) can help in addressing complex and uncertain problem situations within community organisations, in particular Alternative Food Networks (AFNs). Literature has highlighted the importance and benefits of AFNs, but also the complexity and uncertainty underpinning the majority of AFN related problem situations that limit decision making and strategic planning and threaten the long-term sustainability of AFNs. To address this issue, we discuss the use of ST via a VSM intervention within a member-driven food cooperative in Copenhagen, Denmark, and the changes in decision making and the organisational structure of the cooperative. We illustrate the application of the VSM and in particular the methodology for organisational self-transformation within ‘localist green communitarianism’ and ‘nonprofit management’ to tackle issues, enhance democratic and participative decision making, and changes in the organisational structure that foster coordination and cohesion. The implications for COR and Soft OR, limitations and future research directions are also provided.