The stone fruit industry, particularly plum (Prunus domestica) production, is important to the Albanian economy. The Prunus domestica ‘Tropojane’ predominates due to its high and stable productivity, adaptability, and superior organoleptic qualities. Assessing phytosanitary status of this fruit plant is important, to ensure sustainable production and preserve genetic resources. During the spring seasons of 2022, 2023 and 2024, 129 samples of ‘Tropojane’ plum were collected across the regions of Tropoja, Kukës, Has, Puka, Durrës, Paskuqan, and Kamëz of Albania. All samples were tested by ELISA, PCR, and qPCR to detect plum pox virus (PPV), the most destructive virus infecting plum, and to screen for additional stone fruit viruses including Prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), apple mosaic virus (ApMV), and apple chlorotic leafspot virus (ACLSV). ELISA tests demonstrated that PPV was present in 35.5% of the samples, whereas RT-PCR and RT-qPCR assays detected PPV in 45.6% of the samples, confirming greater sensitivity of the PCR assays for virus detection. No infections with other assessed stone fruit viruses were detected. PPV identity was confirmed by sequencing, and phylogenetic analyses showed that the Albanian isolates clustered within the Rec strain group, also indicating their possible regional origin. Meristem culture was employed as a sanitation strategy for PPV-infected explants. Differences in regeneration capacity among plum populations were observed, yet stable in vitro cultures were established in all cases, and molecular diagnostics confirmed that regenerated plantlets were PPV-free. In vitro shoots were successfully subcultured, rooted, and acclimatized. These results highlight the need to conserve native plum germplasm, and enforce the use of certified planting material, to ensure the long-term preservation of autochthonous cultivars, while preventing further spread of PPV.