This study evaluates the capacities of agrarian reform beneficiary organizations (ARBOs) to participate in value chains using data from three pilot areas in Mindanao of the Project Convergence on Value Chain Enhancement for Rural Growth and Empowerment project of the Department of Agrarian Reform. The study found low levels of organizational maturity and weak alliances among farmer organizations in the country. Thus, small farmers’ participation in higher value chains has been limited, with only members of matured organizations benefitting from value chain initiatives. To capacitate farmer organizations, the study recommends that the government pool its resources and efforts and develop strategic capacity-building interventions. Achieving organizational maturity requires farmer members to commit to their ARBO through equity participation. Alternative ownership rights structure may also be considered to encourage members—both commercial and subsistence farmers—to participate and invest in cooperatives. Another strategy is to enable farmer organizations to establish enterprises that will generate income for their members. Lastly, it is also important for organizations to strengthen social relations through regular meetings, collective activities, and patronage incentives to build trust among members.