Numerous food safety incidents have gained public attention and motivated consumers to seek safer and healthier products. Some governments have responded by enacting legislation to regulate the traceability of agricultural products and enhance food safety. To elucidate factors that affect consumers’ health and safety perceptions and repurchase intention for certified traceable fresh food, this study applied institutional trust theory to explore the effects of institutional trust (i.e., trust in government, certification organizations, producers, and retailers) on consumers’ food safety and health perceptions and repurchase intention. This study was conducted in Taiwan and enrolled 393 consumers who purchased certified traceable fresh food as survey participants. Structural equation modeling and multiple and stepwise regression analysis were performed for data analysis. The results indicated that trust in government, certification organizations, food producers, and food retailers was positively related to food safety perception; trust in certification organizations, food producers, and food retailers directly influenced food healthiness perception, whereas trust in government did not have a direct influence. Furthermore, trust in certification organizations and food producers influenced repurchase intention, whereas trust in government and food retailers did not. Based on these results, the current study provides some practical suggestions for traceable fresh food marketers to use institutional trust to improve consumers’ food health and safety perceptions and repurchase intention.