Tomato brown rugose fruit virus (ToBRFV), belonging to the genus Tobamovirus, is a highly-virulent emerging virus species, causing disease outbreaks and significant crop losses worldwide. No effective measure has been identified to control ToBRFV infection. Therefore, the objectives of this study were to investigate the effectiveness of three seed disinfection treatments on the elimination of ToBRFV in tomato seeds and their effect on seed quality. Seeds extracted from ToBRFV-infected fruits were treated with 2% hydrochloric acid (HCl) for 30 min, 10% trisodium phosphate (TSP) for 3 h, dry heat at 72 °C for 72 h, or their combinations; then, the seeds were tested for the presence of the virus using serological, molecular, and biological assays. Parallel treatments of seeds in distilled water (hydropriming) or untreated seeds were included for comparison. The quality of the treated seeds was also evaluated in terms of seed standard germination, mean time to germination (MTG), and seedling growth. Seeds extracted from ToBRFV-infected fruits had a 100% contamination rate. Treatment of ToBRFV-contaminated seeds with 2% HCl for 30 min or 10% TSP for 3 h resulted in a 100% disinfection rate, while heat treatment at 72 °C for 72 h or hydropriming treatments resulted in a 0% disinfection rate. Furthermore, seed treatment with HCl or hydropriming for 3 h significantly improved seed germination percentage, reduced MTG (faster speed of germination), and increased seedling length. In conclusion, seed treatment with 2% HCl for 30 min not only resulted in a 100% disinfection rate of seeds from the ToBRFV but also improved seed quality of tomato compared to untreated seeds.