Agri-food products undergo very complex journeys until they reach our kitchens. Initial challenges start on the farm and continue in processing, storage, transport, distribution and even consumption. Besides the origin of the raw materials, value chain processes influence the quality of our food and finally our health. Modern digitalization endeavors, however, provide great opportunities to ensure the quality and authenticity of agri-food products. Development of digital fingerprinting approaches enable on-the-spot examinations providing comprehensive information about the product. This study aims to provide insights about recent results of Near Infrared Spectroscopy (NIRS) supporting the monitoring of food supply “from farm to fork” – and beyond. Numerous studies have demonstrated in our work the efficacy of NIRS across different stages of the food supply chain in providing comprehensive insights into tested materials, which has proven that NIRS is one of the most comprehensive tools to evaluate the old saying, “you are what you eat”. The most recent findings in the field of nutritional neuroscience even enable the technique to move beyond the confines of food quality assessment to directly correlate nutrition and health.