The Forest Stewardship Council initiated a pilot Forest Certification for Ecosystem Services (ForCES) project from 2011 to 2017 to improve and promote sustainable forest management addressing a range of ecosystem services. Three sites in Indonesia were studied in the pilot. Whilst the development of the certification standard was largely by a partnership between the certification standard organization, civil society and research organisations, implementation and monitoring of the impact of this voluntary sustainability standard will entail interaction with state regulations. This study sought to understand how certification and state regulations concerning ecosystem services in Indonesia interplay, particularly in the agenda setting and negotiation stage. Using the conceptual lenses of transition theory and state and non-state market-based governance, the interrelationships between ecosystem services certification and regulations were found to be both complementary, supporting and antagonistic. The majority were complementary. Antagonism occurred where regulations do not accommodate land use issues and due to different contradictory state regulations. The voluntary instruments were developed largely in the absence of state involvement and without any substitution with regulatory standards. Given the increasing proliferation of voluntary market-driven initiatives at farm, forest concession and landscape level, stakeholders developing and managing voluntary standards need to collaborate with national and local governments to create synergy to enable their acceptance, adoption and effectiveness to positively enhance the conservation of ecosystem services through incentivizing market-based instruments.