Hydrogen peroxide (H2O2) is an oxidizing agent used to disinfect recirculated irrigation water during the production of organic crops under controlled environmental systems (e.g., greenhouses). To characterize the phytotoxic effects and define a concentration threshold for H2O2, three microgreen species [arugula (Brassica eruca ssp. sativa), radish (Raphanus sativus), and sunflower (Helianthus annuus ‘Black Oil’)], and three lettuce (Lactuca sativa) cultivars, Othilie, Xandra, and Rouxai, were foliar sprayed once daily with water containing 0, 25, 50, 75, 100, 125, 150, or 200 mg·L−1 of H2O2 from seed to harvest under greenhouse conditions. Leaf damage was assessed at harvest using two distinct methods: 1) the percentage of damaged leaves per tray and 2) a damage index (DI). Applied H2O2 concentrations, starting from 25 mg·L−1, increased the percentage of damaged leaves in every species except ‘Black Oil’ sunflower, which remained unaffected by any applied concentration. Symptoms of leaf damage manifested in similar patterns on the surface of microgreen cotyledons and lettuce leaves, while mean DI values and extent of damage were unique to each crop. Fresh weight, dry weight, and leaf area of all crops were not significantly affected by daily H2O2 spray. Identifying how foliar H2O2 damage manifests throughout the crop, as well at individual cotyledon or leaf surfaces, is necessary to establish an upper concentration threshold for H2O2 use. On the basis of the aforementioned metrics, maximum recommended concentrations were 150 mg·L−1 (radish), 100 mg·L−1 (arugula) for microgreens and 125 mg·L−1 (‘Othilie’), 75 mg·L−1 (‘Rouxai’), and 125 mg·L−1 (‘Xandra’) lettuce.