Our work focuses on the Forest Stewardship Council (FSC), one of the most stringent, but also contested certification schemes for sustainable forestry. Responding to criticisms concerning inconsistency at the national level, FSC-International recently increased the prescriptiveness of its international standards, including the development of biodiversity-related International Generic Indicators (IGIs). We aim to understand recent efforts in Canada, Sweden, and Russia to revise national-level FSC standards in line with biodiversity-related IGIs. What were the key factors influencing the standard-development process and its outcomes? Were stakeholders satisfied with the negotiations and what was finally achieved? The data were drawn from semi-structured interviews with key participants, a comparative analysis of biodiversity-related indicators in newly approved FSC standards, and analysis of reports prepared by national FSC offices. We applied the Institutional Development and Analysis framework within a complex systems approach to identify multiple interconnected factors that shaped standard-development processes and outcomes in each country. Our findings indicate that despite persistent efforts of FSC-International to harmonize FSC standards across all countries, there are a number of interrelated key factors, which influence outcomes at the national level. Four common clusters of endogenous factors were key to standard-development processes and outcomes in each of these countries: process-related factors, biodiversity-related actions, desired level of control over biodiversity-related outcomes, and adequacy of available knowledge about biodiversity. Forest governance was the only common cluster of key exogenous factors in Sweden and Russia, many of which were identified as constraining the emergence of a consensus-oriented negotiation process. Our findings indicate that efforts to enhance the consistent performance of forest certification for biodiversity conservation require an improved understanding of negotiation outcomes as the emergent products of interactions between multiple exogenous and endogenous factors. This implies a need for a greater focus on process management aspects during future negotiations.