The agri-food supply chain (AFSC) is an extremely complex structure that comprises a series of events from farm-to-fork. Additionally, there is a wide range of information and material flows that require to be managed, which are seen as the knowledge flow in the AFSCs. It is expected that the use of knowledge governance mechanisms (KGMs) will help in enhancing AFSC performance. To examine the impact of KGMs on AFSC performance, a mixed methods research design was applied. First, semi-structured interviews were conducted to collect data. Then, themes were generated through thematic analysis. Afterwards, relationships between KGMs and AFSC performance were built by using total interpretive structural modelling (TISM). Finally, questionnaire-based structured interviews were undertaken to evaluate the empirical and theoretical findings further. The research results indicate that trust-, reciprocity-, market-, and contract-based KGMs have positive effects on product quality, efficiency, flexibility, responsiveness, and process quality of AFSC. Furthermore, market-based KGM, located in the lowest level in the TISM hierarchy, should be given additional focus due to its role as a key force driving the higher level of AFSC performance and other KGMs. The findings provide AFSC practitioners with useful guidance on how the relationships between KGMs and AFSC performance should be managed to improve the performance of AFSC.