Apple production in the Republic of Macedonia is an important sector that highly contributes to theeconomy in terms of employment and income, especially for the small farmers in Prespa Region. Despitecooperatives’ efforts and governmental support to attract members through the provision of inputs,technical advices and other incentives to farmers, membership adherence is low and slow. The TransactionCost Economics Theory (TCE) provided the basis for this study where the choice is conditioned by relativecomparative advantage in terms of lower transaction costs. Based on the research, following conclusions are underlined: a. from the perspective of farmers andthe cooperatives there are factors that positively influence the choice of cooperative membership; b. fromthe cooperative’s side, some of the positive influences are its regular flow of price information, constanttechnical advices and secured market; c) for farmers who aim at increasing production and improving theirincomes, membership to cooperative signifies security of accessing cheaper inputs especially chemicalfertiliser, security of market for the produced apples and higher frequency of transaction cost. Farmers’choices are not exclusive to one type of structure or the other. Farmers can transact with the cooperative andtrader at the same time, influenced by the differences in the price among the “Idared” and “varieties”. Bothof them, members and non-members are limited connected to the “middlemen” in choice of transactions.