Ozonated water has been extensively used in the food industry as an effective sanitizer to prolong the shelf life of fruit and vegetables during the postharvest. Recently, the disinfection of water used in primary production has been a critical point in preventing plant losses during the growing of the crop, especially in the nursery crop. In this study two different irrigation treatments have been used: ozonated water (OW, 750 mV), and electrolyzed water (EW, 495 mV), compared to a control treatment using water without any sanitizer treatment, in capsicum seedling plants grown under greenhouse conditions. The results showed the control to have the highest Ca, Mg, and Zn values with respect to the OW and EW treatments. However, no significant differences were observed in these minerals in the vegetal plant tissue. Capsicum leaves, irrigated with EW and OW, showed a minor content in B and Na. Moreover, the sanitizing treatments provided plants with a higher number of leaves. Sanitizer treatments did not affect the net photosynthesis or antioxidant compounds, total phenolic compounds, nor the vitamin C. At day 49 lower DHAA and lipid peroxidation were observed in treated samples. A higher catalase activity was measured in OW and EW irrigation treatments compared to the control, preventing the lipid per oxidation. Additionally, OW and EW reduced the microbial load in the water (E. coli and total Enterobacteriae) and OW reduced the mould and yeast of water and the mesophilic load of capsicum seedlings.