Background Food supply chain companies are major link for safe food production and distribution. Food safety ensures reduced food losses and, therefore, contributes to food security. Although there have been extensive studies on the food industry with different perspectives, no study has so far been conducted on the challenges in terms of the food security. The present study is a qualitative one conducted in 2019 in one of the largest agricultural production chain companies in Khorasan Razavi province, Iran. Results The research method was based on the conventional content analysis. Triangulation method was used for the data collection being a combination of the participant observations, focus group discussions (17 managers) and semi-structured interviews with the president of the company. Participants believed that their company plays an important role and has a prestigious position in the food security of Iran. However, the main challenges of the company are regulatory system, food safety risks, market unpredictability, traditional management and sanctions. Conclusions The company is highly resilient to all these challenges; however, the traditional management is still a serious disadvantage. This leads to the managers’ burnout along with the company survival problem, removing unfair sanctions and protecting agricultural development in developing countries is a necessity. In general, paying attention to the modern organizational management of these companies and their survival is an essential policy. For this reason, it is suggested that trust must be established between policymakers and companies on one hand and relationship between the academia and such companies to promote the organizational management on the other hand.