This study aims to investigate the supply chain challenges of public sector agriculture development projects in Bangladesh using the modified Delphi, Best Worst Method (BWM), and Interpretive Structural Modelling (ISM) methods. Based on these three widely acclaimed statistical techniques, the study identified, ranked, and identified interrelationships among the challenges. The study is unique not only in terms of research findings, but also in terms of methodology, as it is the first to use the three MCDM (Multicriteria Decision Making) tools to examine supply chain issues in public sector agriculture development projects in a developing country context. A literature review and two modified Delphi rounds with 15 industry experts’ opinions were applied to identify and validate a list of 11 key supply chain challenges. To determine the priority of the challenges, a panel of eight industry experts was consulted, and their responses were analysed using the BWM. Then, another group of 10 experts was consulted using ISM to investigate the contextual relationships among the challenges, resulting in a five-layered Interpretive Structural Model (ISM) and MICMAC (cross-impact matrix multiplication applied to classification) analysis of the challenges. According to relative importance (global weights), "improper procurement planning (0.213), "delay in project initiation (0.177), "demand forecasting error (0.146)", "lack of contract monitoring mechanism (0.097)", and "lack of competent staff (0.095)" are the top five ranked key challenges that have a significant impact on the project supply chain. Regarding contextual relationships, the ISM model and ISM-MICMAC analysis identified the "political influence" challenge as the most influential, and also independent of the other challenges. The findings are critical for project managers in managing challenges because understanding both relative importance and contextual relationships are required to address the challenges holistically. Additionally, these findings will benefit policymakers, academics, and future researchers.