FPO versus cooperative society, what is the actual difference in running them?

The core difference is who governs you and how much freedom you have. A cooperative society is registered and governed under the state cooperative act, so the state cooperative/registrar department has a strong say, audits and sometimes elections and decisions are influenced by them. A Producer Company FPO is registered under the Companies Act with the Registrar of Companies, so it runs like a private company owned only by farmer members, with a board, professional management and statutory audit, and far less day to day department control. Both keep the one member one vote principle and share profits with members. Day to day, the Producer Company gives faster decisions and easier access to modern credit and grants, but demands stricter compliance (ROC filings, audited accounts, board meetings). The cooperative is simpler to run for a very small group but slower and more politically exposed. Most new FPOs under the scheme are Producer Companies for these reasons. Pick the cooperative only if your group genuinely prefers the older structure and can handle department involvement.