Tomato production in Albania has shown significant growth in recent years, with the total cultivated area in 2019 reaching 6,663 hectares (FAO 2020). The recent identification of Tomato brown rugose fruit virus (ToBRFV) in several greenhouse tomato farms has raised concerns among many growers about a possible outbreak of this virus in Albania. Therefore, this study was conducted to assess the presence of ToBRFV, together with other important tomato viruses that might be present and spreading in Albanian greenhouses. Nine tomato-infecting viruses, i.e., ToBRFV, tomato yellow leaf curl virus (TYLCV), pepino mosaic virus (PepMV), tomato chlorosis virus (ToCV), tomato infectious chlorosis virus (TICV), alfalfa mosaic virus (AMV), cucumber mosaic virus (CMV), tomato mosaic virus (ToMV), and tomato spotted wilt virus (ToSWV), were investigated in ca. 200 samples, and their sequences were analysed using qPCR and sequencing, respectively. Results showed that ToBRFV, ToCV, AMV, CMV, ToMV, and TSWV, were present in the tested samples, with different levels of infection. ToBRFV and AMV were found to be highly prevalent in Fier region, while ToCV was significantly present in Shkodra region. Almost all Albanian viruses’ isolates had showed sequence variations. Valuable insights are now gained by this research on the regional prevalence and distribution of these six viruses in different varieties, contributing to a better understanding of the viral diseases affecting tomato crop in Albania.