The Prunus genus represents one of the main targets for regulating the health status of plants. Individual plant tagging with an implanted microchip may support plant certification or protect property rights, in addition to having research applications. Production of radiofrequency identification (RFID) implants in Prunus spp. plants was performed following two tagging procedures designed to consider Prunus anatomy, histology and grafting techniques. To assay the impact of microchip insertion, measurements of vascular tissue area by image analysis and histological observation were made, confirming the good healing capability of the plant. Moreover, neither production losses nor reduction in growth were noted, suggesting Prunus spp. as a suitable host for microchip implanting. An online database was developed to match microchips with information datasheets that can be read and updated by users to manage the marked plants. The present work concludes that implanted RFID microchips can be efficiently used for identifying, storing and tracking plants to support certification.Highlights► No production losses or reduction in growth with Prunus plants with RFID tags. ► Prunus spp. is a suitable host for microchip thanks to its healing capability. ► Implanted RFID tags can be used for identifying, storing and tracking Prunus plants.