The main aim of this research study was to assess the interactive effects of water deficiency and the inoculation of a growth medium with Beauveria bassiana on plant growth, nutrient uptake, secondary metabolite contents, and antioxidant capacity of Allium cepa. A. cepa seedlings were simultaneously exposed to one of three watering regime treatments (3-day, 5-day, and 7-day watering intervals) and B. bassiana or no-fungus treatment. While the longest watering interval induced reduced plant growth, plants inoculated with B. bassiana had better results than those in the no-fungus treatment. Significant interactive effects (DF = 2.0; p < 0.05) between fungus and the watering regime on P, K, and Fe contents were observed. Remarkably, at the 7-day watering interval, the polyphenol content (64.0 mg GAE/L) was significantly higher in the plants treated with B. bassiana than in the no-fungus-treated plants. The watering interval significantly affected (DF = 2, 6; F = 7.4; p < 0.05) total flavonol contents among the fungus-treated plants. The interaction of the watering interval and B. bassiana inoculation (DF = 2.0; F = 3.8; p < 0.05) significantly influenced the flavonol content in the onion bulbs and the antioxidant activities of onion bulbs in the FRAP assay (DF = 2.0; F = 4.1; p < 0.05).