The Forest Stewardship Council (FSC) standards are becoming increasingly important in sustainable forest governance. In 2016, FSC certified a total forest area of 195Mha across 80 countries. While there is considerable room for expanding FSC's reach, there has been a lack of incentives for producers to seek certification, particularly in tropical countries. Information about existing barriers and challenges to comply with FSC standards are fundamental to promote such incentives. The objective of this study was to explore the main challenges faced by firms in the FSC certification process and discuss their policy implications. This was carried out by analyzing the quantity, spatial distribution, non-compliant principles, potential triggers and thematic areas of non-conformities (NCs) to FSC certification disclosed in the Public Summary Reports of third-party audits in Brazil. More specifically it tried to understand the specific issues to which the NCs were potentially associated to. This study generated descriptive and inferential statistics of a sample of 1086 NCs to FSC standards disclosed in the 110 Public Summary Reports, from which the overall majority were related to the certification of plantation forests that had gone through maintenance audits. The occurrence of NCs was found to be most frequently associated with FSC Principles 4 (26,07%), 6 (21,82%) and 8 (13,72%), which are related to the themes “Community Relations and Worker's rights”, “Environmental Impact” and “Monitoring and Assessment”, respectively. Many NCs were triggered by aspects of forest planning, operation and monitoring, which altogether accounted for 42.91% of all NCs. Problems related to occupational health and safety were also a relevant theme, accounting for almost 20% of the total non-conformities. Findings from the Kruskal-Wallis tests suggest that auditors tended to identify similar NCs, regardless of the geographical region, of the type of forest and of the type of audit (certification or maintenance). Spearman Correlation tests indicated significant relationships between certified forest area and non-conformities with FSC Principles 4 and 7 (Community Relations and Worker's Rights, and Management Plans, respectively). The meaning of this relationship is unclear. Overall, findings corroborate previous studies that found FSC Principles 4 and 6 among the most challenging of the global FSC system. There seems to exist an opportunity for the development of stronger technical guidance and capacity building policies related to community relations, worker's rights, and environmental impacts. If such issues are already challenging in the context of large forest plantations, Brazilian policy-makers should expect small-scale firms to face even higher levels of difficulty, given their lack of financial and human resources. The study concludes by discussing its limitations and suggesting future research avenues.