This article addresses fundamental knowledge of the Back-End of the Coffee Agribusiness System that can influence the final quality of the product, integrating the areas of agronomy, medicine and business. The representation will be made through an ontology that will contribute to clarifying for the scientific community the possible impacts of the use of coffee with compromised qualities in clinical research as well as informing and educating consumers with regard to coffee choice. Six steps were followed 1) Targeted search; 2) Literature review; 3) Systematic search in the target interest of the three areas of literature: agronomy, medicine and business; 4) Field research through six semi-structured interviews with the purpose of validating the research problem; 5) Organisation of knowledge with the aim of forming a common knowledge base as a starting point for ontology and 6) Ontology development. Coffee is one of the most researched substances in the world. There are more than 25,000 scientific articles published just from the clinical point of view (Illy, 2016), but little is available integrating results from clinical research, agronomy and management. Improvements in coffee quality could be developed with the knowledge integration of these areas. The Specialty Coffee Agribusiness System Knowledge Representation will improve subsidies funding for the scientific community because of the importance of using good quality coffee in clinical research. It will also guide professionals in the coffee agribusiness system to produce better quality coffee and offer a common vocabulary for the principal properties and influences during the Back-End process for researchers in the three areas.