Cape gooseberry (Physalis peruviana) is one of the most important crops in Antioquia (Colombia). However, little is known about the viruses circulating in Cape gooseberry in the southwestern region of the province. In this work, the prevalence of seven viruses (PVY, PVS, PVX, TaLMV, PhyVNV, CGIV-1, and PMTV) was tested by RT-qPCR on seed samples, symptomatic and asymptomatic plants from commercial fields from this region, and virus genomes were investigated using high-throughput sequencing (HTS). The results showed the detection of all seven viruses in at least one sample. PMTV was the most prevalent virus as it was found in six seed samples, eight asymptomatic, and ten symptomatic samples. HTS analysis revealed the presence of a new virus species closely related to the genus Trichovirus and tentatively named as Cape gooseberry associated trichovirus (CgaTV). Near full-length genome sequences were obtained for P. peruviana infecting isolates of TaLMV, PhyVNV, and PVY.