There is a growing trend towards small-scale forest operators engaging in certification initiatives in response to growing demands for certified timber. We aimed to analyse whether certified smallholders gain better access to timber markets and better financial incentives. We used three smallholder forest enterprises from Gunungkidul and Kulon Progo districts, Java, Indonesia as case studies of different managerial operations. Two were farmer cooperatives and the other was an external trading company in partnership with village-level farmer groups. Different certification schemes and managerial approaches were analysed whether such factors influenced the ability of smallholders to access certified timber markets and obtain improved offers for their timber. We found that smallholders find it challenging to enter and participate in certified timber markets and to obtain the promised premium prices. The obvious costs of certification and uncertain benefits are major challenges for smallholders. Even when market opportunities are present, certification alone is insufficient to tap into these markets. Certified forest enterprises need dedicated managers with adequate entrepreneurial skills to establish networks and contacts with potential buyers, and to actively seek information on what is specified by certified timber processors.