The transition toward sustainable agricultural production can be supported with improved insight into the performance of existing farming systems. The Sustainability Assessments of Food and Agriculture Systems (SAFA) framework published by the Food and Agriculture Organization (FAO) provides a comprehensive and harmonised framework to assess and compare farming systems. We used the indicator-based SAFA consistent Sustainability Monitoring and Assessment RouTine (SMART) Farm Tool to analyze and compare the sustainability performance of certified organic and fair trade as well as non-certified smallholder farms in Uganda. Using the respective sustainability scores, we analyzed the synergies and trade-offs between sustainability themes using the non-parametric Spearman correlation test. We find that certification is associated with improved sustainability performance of smallholder coffee farms. It enhances the achievement of governance goals through its influences on group organization and collective capacities - this results in positive effects on other sustainability dimensions. Major synergies were observed between social and governance themes, and between economic and environmental themes. Although, the extent and distribution of the synergies and trade-offs varied among farms, they were consistent between the production systems. These results show that the production systems can potentially have more influence on the sustainability performance than certification per se.