Cherry virus A, a capillovirus, can infect different Prunus species and be present as a latent infection in orchards. CVA infection was detected in a Hungarian stock collection of Prunus domestica ‘Besztercei Bt. 2’. In our study, different in vitro virus elimination techniques (thermotherapy combined with shoot tip culture and chemotherapy alone or combined with thermotherapy) were used and compared for their efficiency in eliminating CVA from ‘Besztercei Bt. 2’ plum cultivar. Thermotherapy was carried out at 38/36°C (day/night) in a heat chamber followed by the excision of 1–2 mm long shoot tips for plant regeneration. As a chemotherapy agent, ribavirin or zidovudine was added to the multiplication medium at two different concentrations with or without two weeks of thermotherapy pretreatment. The plum shoots tolerated 14–18 days of heat treatment, 64% of the plants regenerated from shoot tips, and 75% of the tested regenerated plants were confirmed by RT‒PCR to be CVA-free. Ribavirin and zidovudine did not negatively affect the survival of the plum shoots at any applied concentrations. Zidovudine alone was not able to efficiently eradicate virus from the treated plantlets, but when zidovudine was combined with heat treatment, the number of CVA-positive plants decreased to 60%. In contrast, ribavirin alone was very efficient at eliminating CVA from all the tested plants when used at a concentration of 25 mg L− 1. To our knowledge, this is the first report of eliminating CVA from Prunus sp. via in vitro techniques.