Endothelial dysfunction is commonly associated with a cardiovascular event, such as myocardial infarction. Myocardial infarction is marked by an ischemia/reperfusion (IR) phenomenon associated with endothelial dysfunction, contributing even more to future cardiovascular events. Although the supplementation with L-citrulline and nitrate from watermelon and beetroot have been used to improve vascular function, the effect of microencapsulated watermelon rind (WR) or its co-ingestion with beetroot (WR + B) on endothelial IR injury has not been addressed. Therefore, this study aimed to investigate the effect of a single dose of WR and WR + B on IR-induced macro-and microvascular dysfunction. In a randomized, crossover, placebo-controlled study, 12 volunteers underwent macro (flow-mediated dilation) and microvascular (muscle oxygen saturation) assessment and blood collection (to measure L-citrulline, L-arginine, nitrate and nitrite) before and after 20 min of blood occlusion in WR, WR + B and placebo conditions. Prolonged ischemia induced endothelial dysfunction in the macro but not in the microvasculature. The WR and WR + B supplementation significantly restored FMD after IR injury compared to the placebo (p < 0.05). However, there was no significant difference between WR and WR + B in the macrovascular function (p > 0.05). Plasma L-citrulline, L-arginine, nitrate, and nitrite significantly increased (p > 0.05) after WR and WR + B supplementation compared to the placebo. A single dose of WR and WR + B effectively minimizes IR-induced macrovascular endothelial dysfunction in healthy individuals. Beetroot co-ingestion with watermelon did not provide an additional effect of endothelial dysfunction induced by IR (NCT04781595, March 4, 2021).