Sustainable coffee production promises to improve production techniques and enhance the socioeconomic conditions of smallholder farmers. Using primary survey data from 659 coffee producers in Honduras, this study assesses the impact of voluntary sustainability standards (VSS) on the technical efficiency of smallholder coffee production. The article uses the Stochastic Production Frontier Analysis model to analyze and compare the technical efficiency (TE) of certified and non-certified coffee producers. To provide reliable comparability between groups, the dataset was balanced using Covariate Balancing Propensity Score (CBPS). The results show that the mean technical efficiency was 52.86% for pooled certified farmers and 55.56% for non-certified smallholder coffee producers. Specifically, the technical efficiency of 4C farmers was 51.58%, 53.82% for the Fairtrade group, 60.56% for RA farmers, and 60.15% for the UTZ group, indicating substantial inefficiencies in the coffee production of the different certified groups. Results from Tobit’s model for the determinants of TE indicated that variables such as the age of the household head, access to credit, and training attendance are among the main factors that significantly drive the technical efficiency of certified and non-certified farmers. Based on the findings, enhancing education opportunities, improving infrastructure for better market access and farm management, and expanding credit access are recommended to improve efficiency in the study area. Honduran smallholder coffee producers have considerable potential to increase output with existing technology by improving their technical efficiency. Therefore, stakeholders’ efforts should focus on enhancing efficiency levels and capitalizing on potential gains for both certified and non-certified farmers, to ultimately improve the farmers’ livelihoods.