This study clarified the changes in forest management and timber marketing after acquisition of the Indonesian Ecolabelling Institute's community-based forest certification through a case of Gunung Kidul, Yogyakarta, Indonesia. The certification had good effects to improve forest management, although any apparent effects on timber marketing were not observed. Meanwhile, this study observed the potential of certification to help with the acquisition of the Indonesia Timber Legality Assurance System certification under the Voluntary Partnership Agreement of Forest Law Enforcement, Governance and Trade. In order to disseminate the forest certification to small-scale forestry it is necessary to promote selling certified timber and generate a premium price for smallholders. In particular, the challenges of Chain of Custody and the inherent nature of small-scale forestry should be addressed. The dissemination of national forest certification, which provides more appropriate benefits for smallholders and provokes their motivation for sustainable forest management, still remains a big challenge in Indonesia.