The effectiveness of intermittent corona discharge plasma jet (ICDPJ) treatment over continuous mode for the decontamination of cherry tomatoes was evaluated. Microbial contaminants, namely aerobic bacteria, yeasts and molds and coliform bacteria, were detected in tomatoes in the range of 2.49–3.05 log CFU/g. Tomatoes were treated with corona plasmas generated using 8 kV DC power supply and at 2.0–4.0 A currents. A distance of 60 mm was maintained between the discharge electrode and the sample surface during plasma treatment, with a maximum treatment time of 2 min. In contrast to CDPJ-treated tomatoes in continuous mode, a maximum surface temperature of 33.7 °C and no plasma-induced alterations in tomato color and firmness were observed in ICDPJ-treated tomatoes. The ICDPJ treatment decreased the contaminants loads by 0.68–1.02 log CFU/g at 2.0 A, by 1.42–1.71 log CFU/g at 3.0 A, and by 2.00 log CFU/g to non-detectable level at 4.0 A. There were no significant differences in terms of taste, flavor, color, texture, and total acceptance scores between the untreated and ICDPJ-treated samples for 2 min at 2.0, 3.0, and 4.0 A. During storage at 25 °C for 15 days, the samples treated using the ICDPJ at 3.0 and 4.0 A currents exhibited significant extension of shelf life for up to 10–15 days, in contrast to untreated controls (6 days).