Fermented foods are consumed in diets worldwide and can be an important part of a dietary strategy to prevent and manage cardiometabolic diseases. However, precise associations between the consumption of fermented foods and cardiometabolic health have not been well established. This could be partly due to the difficulty of accurately capturing their intake through self-report dietary assessment methods. This thesis set out to identify food intake biomarkers (FIBs) for the habitual intake of fermented foods, which can act as more objective measures of intake. In addition, several candidate FIBs for dairy foods that were identified from non-targeted, controlled intervention studies needed to be validated under free-living conditions. These aims were achieved using data from a free-living cohort in the Netherlands (NQplus). Alongside, associations between fermented food and dairy food intake, biomarkers, and cardiometabolic factors were explored, revealing the diverse metabolic effects of these foods.