The COVID-19 pandemic had affected all food systems in West Africa. The first outbreak of this disease in Benin was reported by the government on the 16th of March, 2020. The current work aimed to determine the Non-communicable diseases (NCDs) occurrence, food accessibility and handling practices and the dietary behaviors during SARS-CoV-2 pandemic in Benin and the relationship between these components. Then, a systemic survey was undergone with 300 respondents in North-Benin. Data analyzes were performed using SAS software. A hierarchical cluster analysis based on the characteristics of the households and their food access, utilization and handling practices on the most significant components of AFC was then performed. It appears that hunger, hunger consequences and food insecurity level had been exacerbated by COVID-19. About food access during COVID-19, 80% of respondents found that their dietary needs were challenged by the restriction measures. This challenge affects infants as well as children, pregnant women, breastfeeding women, elderly people and people with a chronic disease. Price of food products had increased on the local market and limit the ability of 80% of household to acquire sufficient and safe food. The factorial correspondence analysis of the dietary behaviors and food handling practices during SARS-CoV-2 pandemic in Benin discriminated three groups of households corresponding to 3 types of dietary behaviors and food handling practices. The main NCDs reported were cardiovascular disease, diabetes and chronic lung illnesses. One Heath multi-sectorial action plans for food and nutrition security are needed to reduce the vulnerability of food systems and households to emerging infectious diseases.