•ISO-FOOD ontology – a new way of representing isotopic data for food research.•Defines metadata needed for isotopic characterization.•Describes a powerful technique for organizing and sharing stable isotope data across Food Science. To link and harmonize different knowledge repositories with respect to isotopic data, we propose an ISO-FOOD ontology as a domain ontology for describing isotopic data within Food Science. The ISO-FOOD ontology consists of metadata and provenance data that needs to be stored together with data elements in order to describe isotopic measurements with all necessary information required for future analysis. The new domain has been linked with existing ontologies, such as Units of Measurements Ontology, Food, Nutrient and the Bibliographic Ontology. To show how such an ontology can be used in practise, it was populated with 20 isotopic measurements of Slovenian food samples. Describing data in this way offers a powerful technique for organizing and sharing stable isotope data across Food Science.