Tomatoes have high nutritional and economical value and its deterioration start after harvest. They need proper treatments to increase and maintain quality as well as shelf life. The objective of this study was to determine the effect of iron, iodine and selenium on quality, shelf life and microbial activity of cherry tomatoes. Iron (1 mg/L), iodine (1 mg/L) and selenium (1 mg/L) were supplied with nutrient solution for five weeks prior to harvest. Then, cherry tomatoes were stored at 5 °C to assess quality, shelf life and microbial activity. The highest Ca content (p < 0.05) revealed in selenium-treated cherry tomatoes. Lower respiration and ethylene production were showed in selenium-treated cherry tomatoes both harvest time and after storage compared with iron and iodine treatments. At harvest time and after storage, the respiration were 1.29 (p < 0.05) and 0.62 mL/kg/hr (p < 0.01), respectively in selenium-treated cherry tomatoes. Moreover at harvest time and after storage in selenium-treated cherry tomatoes, the ethylene production was 2.11 and 0.87 μL/kg/hr (p < 0.01), respectively. The lowest fresh weight loss, the longest shelf life (p < 0.01), the least fungal incidence rate and microbial activities were found in selenium-treated cherry tomatoes. The longest shelf life of selenium-treated cherry tomatoes was 22 days. Selenium-treated cherry tomatoes' firmness increased (16.82N) at harvest time (p < 0.05) and it was significantly retained (12.70N) after storage (p < 0.01). Color development and lycopene content were more suppressed by selenium treatment after storage than iron and iodine treatments. Titratable acidity, vitamin C and soluble solids increased in selenium-treated cherry tomatoes after storage. Based on results, selenium-treated cherry tomatoes have significant potential to increase and maintain quality and shelf life.