Abstract Recent changes in European Union plant health regulations require diagnostic laboratories to obtain ISO/IEC 17025 accreditation for all tests on regulated pests conducted under official controls. However, meeting all requirements of this standard is challenging due to the vast number of pest, host, and matrix combinations that require test validation and proficiency testing. In plant virology, adopting a risk-based systems approach to validation can help to meet ISO/IEC 17025 accreditation requirements. This approach acknowledges that workflows, which may consist of single or multiple tests, are used for the detection and identification of specific viruses, viroids, and phytoplasmas. For each test within a workflow, validation is determined through a risk analysis based on its specific purpose, while the entire diagnostic process is validated through the combination of tests. This approach could fit within the definition of a “flexible scope” as defined by the European co-operation for Accreditation. When combined with diagnostic expertise and contextual understanding in plant health diagnostics as well as proficiency testing at the method level, this approach improves overall diagnostic proficiency in a cost-effective way and may facilitate accreditation and compliance with plant-health regulations in the European Union.