The study of institutions in the agro-food systems is gaining momentum since it represents an intricate and undoubtedly relevant case study as concerns intermediate-product markets. Moreover, traditionally there is a problem of organization among farmers mainly due to the scarce attitude to pool decisional and property rights on input and/or output. According to the Transaction Costs Economics framework, the paper aims to investigate which are the main drivers of the collective forms of organization in the Italian agro-food system, paying particular attention to transaction costs’ attributes and to the increasing role played by the institutional environment as well. The choice to join to cooperative or producer organization is conceptualized as a governance structure choice, also paying attention to the complementarity between the two alternatives. Based on the Italian version of the Farm Accountancy Data Network, bivariate probit and multinomial are estimated in order to account for three organizational alternatives (participation in cooperative, in OP and join participation in all the three alternatives) and to test the complementarity between the two organizational forms entailed.