Tree tomato or tamarillo (Solanum betaceum Cav.) is an important sub-tropical tree that is cultivated for its edible fruits. The main challenges to tree tomato production are diseases, pests, and drought, with viruses causing the most significant economic losses. The plant is reported to be infected by up to 20 viruses in different parts of the world. The aim of this survey was to establish the distribution of PVY in tree tomato, and assess the prevalence. Two surveys were conducted between 2018 and 2019 across three agro-ecological zones―upper highland, lower highland and midland―within nine major tree tomato-producing counties in Kenya. Leaf samples with virus symptoms were collected from 26 farms. Farms in the midland and lower highland zones exhibited more severe symptoms. Three other viruses TMMoV, Ethiopian tobacco bushy top virus and its associated RNA satellite, and potato spindle tuber viroid were discovered using next generation sequencing. Reverse transcription PCR revealed PVY to be present in 46% of farms visited. The rest of the viruses were all found to occur in mixed infection with PVY. Partial coat protein sequences from Sanger revealed a high percentage similarity, 97% to 98%, with PVY recombinant strain N:O. There were no recombinant junctions identified on any of the sequences. These findings highlighted the widespread occurrence of PVY in Kenyan tree tomato farms. The detection of mixed infections involving PVY underscores the potential for increased disease severity and economic impact. This study provided important baseline data for the development of effective virus management strategies in tree tomato production.