We are experiencing an acceleration in the global drive to converge consumption and production patterns towards a circular and more sustainable approach to the agri-food system. To meet the challenge of reconnecting agriculture, environment, food and health, data from heterogeneous sources and formats need to be integrated and exploited. In this context, ontologies may play a relevant role as they provide a formal representation of knowledge and structure for integrating data. We present a new domain ontology on food and bio-products engineering for data integration in a circular agri-food system. This ontology is based on a core model for a generic process, the Process and Observation Ontology (PO2), which has been specialized to provide the required vocabulary to describe any biomass transformation process and to characterize the food, bio-products and wastes involved as inputs and/or inputs of these processes. Much of the vocabulary comes from authoritative references such as the European food classification system (FoodEx2), European Waste Catalog (EWC) and other international nomenclatures. The ontology is built using Semantic Web standards, aiming to be compliant with the Findable Accessible Interoperable Reusable (FAIR) principles and willing to provide system interoperability and softwaredriven intelligence. This ontology may provide the link between the different drivers (environmental, socioeconomic, nutrition and health) involved into the food system.