This systematic map explores the role of sustainability certification schemes and labels in reducing greenhouse gas emissions across biobased value chains. With increasing global and EU interest in transitioning to a sustainable bioeconomy, these certification mechanisms are seen as critical tools for promoting low-emission practices. This review maps the available evidence regarding the effectiveness of certification schemes, examining sector-specific variations and identifying knowledge gaps. A comprehensive search strategy was employed across three major databases and grey literature sources, yielding 41 relevant articles. There are significant disparities in the evidence on the impact of sustainability certification schemes and labels on greenhouse gas (GHG) emissions across biobased sectors. Agriculture has the most data, but studies are heavily focused on organic systems, limiting broader conclusions. Most research is concentrated in Southeast Asia and Europe, reducing generalizability to other regions. Additionally, most studies focus on the production stage, leaving value chain phases like processing and disposal under-represented. Knowledge gaps exist across sectors, certification schemes, and life cycle stages, highlighting the need for further research. While some schemes incorporate GHG management tools, evidence on their effectiveness remains insufficient and context-dependent, warranting more robust, targeted research. Though this research looked at all biobased feedstocks, it did not review schemes and labels specifically targeting biofuels, which presents an avenue for future research.