Improving food safety and hygiene is integral to the successful attainment of the Sustainable Development Goals (SDGs). Foodborne diseases continue to impose a high burden on low-and middle-income countries (LMICs), particularly children under five years, and meeting stipulated conditions for both domestic and export markets can be challenging. This paper reports a situation analysis exploring the challenges faced in the food safety sector in LMICs, using Malawi as an example. The analysis used a desk and policy review, literature search, key informant interviews, and focus group discussions to provide national data, which was then subject to thematic analysis. The analysis established there is a significant threat to public health and market access due to uncoordinated, outdated or incomplete regulatory framework, poorly defined mandates, limited infrastructure, lack of equipment and skilled personnel, inadequate resources, and limited awareness and ability to comply with standards. Food safety and hygiene improvements must strike a balance between market access gains and protection of public health. To achieve this, the sector requires effective integration at national level in food security, nutrition, health, economic development, agriculture, and poverty reduction. Solutions for each country must be context-specific and take into consideration national realities if they are to be successful.