The industrial research project on food traceability and safety presents its experimental development activities conducted at the laboratory scale. The aim is to enable a subsequent technological and competency transfer to the production sector. The selected food categories include bakery products, dairy products, meat-based products, preserves, and fish products. Various samples were analyzed, including finished and semi-finished products, raw materials, and swabs from food contact surfaces, production equipment, and operators. Chemical, microbiological, and molecular biology analyses were conducted in the laboratories of GRUPPO MAURIZI SRL. Initially, complex analytical panels were established for each food matrix, including hygiene indicator microorganisms, pathogens, and chemical contaminants. From the results, several specific marker parameters were identified for finished products, raw materials, production environment surfaces, and operators within the different food categories examined. These marker parameters were derived from the non-conformities detected for each matrix and the risk analysis of production processes. The analyses resulted in detailed analytical plans capable of identifying quality indicators (markers). Based on this data, FOODIA, a software application, was created to generate a sampling plan for food companies. This plan intersects food regulations, analytical markers identified from empirical studies on food products, and risk analysis. This is facilitated by the software’s database, which will be populated with data related to food regulations and analytical markers for each food matrix.