Forage peanut (Arachis pintoi) is one of the forage crops best adapted to tropical agroecosystems where it is used as ground cover in urban areas and slopes, in the preservation of soils cultivated with coffee, African oil palm and citrus and as animal feed in combination with gramineous plants. A. pintoi is considered to be highly resistant to plagues and diseases; however, in recent years there has been a marked increase of plants showing symptoms typical of viral infection. In this work, Next Generation Sequencing (NGS) was used to confirm the presence of virus in symptomatic A. pintoi plants collected in urban areas in Medellín (Colombia). Transcriptome analysis revealed the presence of 3,291,089 reads related to viruses in the families Potyviridae, Luteoviridae and Alphaflexiviridae and resulted in the complete genome assembly of Peanut mottle virus (9707 nt), Turnip yellows virus (5578 nt) and two variants of a virus with phylogenetic affinity to the genus Allexivirus. These two variants lack ORF6 present in Allexivirus and probably belong to an uncharacterized genus within the family Alphaflexiviridae. The presence of at least three viruses infecting A. pintoi in Colombia highlights the importance of starting a germplasm clean-up program of the plant material used as seed in this crop.