Agro-food quality certification has been gaining greater importance, because it contributes to both agricultural sustainability and food quality. However, small-scale farmers in developing countries have difficulties in obtaining certification and the economic benefits acquired from certification are unclear. This paper investigates the effects of agro-food quality certification on the farm performance which is indicated by profit, yield and price. The impacts of agricultural organizations, farmer cooperatives and agricultural companies in particular, on the adoption of certification by farmers are explored. We also investigate the effects of organizations on the farm performance of certified farmers. A dataset of 410 vegetable farmers in China is applied, and the propensity score matching (PSM) method is employed in the empirical analysis to address selection bias and reverse causality. Our study finds that, overall, the adoption of certification does not significantly influence farm performance. Cooperative membership positively influences the adoption of certification and the farm performance of certified farmers, while contract farming does not generate additional benefits for certified farmers.