The exchange of fruit tree propagation material to different growing regions and countries is a primary source of new pests and pathogens, particularly graft-transmissible viruses and viroids affecting Prunus species worldwide. Traditional procedures often cannot effectively quarantine pathogens and pests with unknown etiology, prompting the study of alternative procedures including those based on tissue culture techniques. In vitro shoot-tip grafting (STG), also called micrografting, consists of aseptically grafting a small shoot-tip onto an in vitro rootstock seedling and is often used to produce virus-free plants. In this study, an improved STG procedure for obtaining and introducing virus-free peach and Japanese plum plants is presented as an alternative to standard quarantine methods. The shoot-tip source is critical for STG success. Two viruses (Apple chlorotic leaf spot virus, Prunus necrotic ringspot virus) and a viroid (Peach latent mosaic viroid) were successfully eliminated in nearly 100% of the micrografted plants using buds from contaminated plants, grafted onto rootstocks forced in vivo at 35°C, as shoot-tip source. The subsequent development of healthy plants for tested peach and Japanese plum cultivars demonstrates the suitability of this method for safe transport of plant material.