Independent smallholders represent more than 3.1 million hectares of all palm oil plantations in Indonesia. However, they receive inadequate attention from sustainability initiatives, deforestation and palm oil production discussions. Meanwhile, evidences show that by collaborating voluntarily in organizations and building linkages with public and private stakeholders among institutional arrangements, farmers have opportunities to access productive assets for expanding their capacities, to seize economic changes, and policy making. Thus, the research answers the key point relationships of the organization of smallholders to meet sustainable certification system. The analysis was conducted in three districts by using structural equation models. The study indicates that there was, directly and indirectly, an effect of the farmers’ organization for achieving sustainability. However, none of independent smallholders in the analysis site participated in the farmers’ organization. The farmers’ organization is also proven to have a positive effect on the legality and a positive indirect effect on the sustainability through the legality. In the farmers’ organization, providing information to relevant stakeholders is in line with the applicable provisions, except on the confidential subject which is important for sustainability. The most important aspect with regard to the legality is the stakeholders’ agreement on management and monitoring of the environment.