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Indonesia is a significant producer of shallots, and the country frequently cultivates three distinct varieties: Bima, Trisula, and Sumenep. Each cultivar exhibits distinct characteristics, specifically when grown under suboptimal conditions. Several studies showed that insufficient watering intervals (WIs) can lead to drought stress, while excessive levels often lead to inundation. To investigate the effects of cultivar and WI on shallot growth and quality, this study employed a split-plot design with main plots and subplots with four repetitions. The main plots consisted of cultivars (Bima, Trisula, and Sumenep), while the subplots comprised WIs (once in 1 day, 2 days, and 3 days). The results showed that there was an effect of interaction between cultivars and WIs on growth (proline [126.15 mg 100 g−1]) and quality (quercetin [3.8739 mg g−1], rutin [0.2080 mg g−1], and kaempferol [1.209 mg g−1]). However, there was no effect on the number of tillers, shoot/root ratio, water content, number of tubers, tuber weight, and total flavonoid.