Biofortification of garlic and onion plants with selenium and arbuscular mycorrhizal fungi inoculation are considered beneficial for producing functional food with anticarcinogenic properties. The effects of arbuscular mycorrhizal fungi (AMF) inoculation, sodium selenate foliar application, and the combination AMF + selenium (Se), compared to an untreated control, were assessed regarding the bulb yield, biochemical characteristics, and mineral composition. AMF + Se application resulted in the highest yield, monosaccharides, and Se content in both garlic and onion bulbs; and an increase of ascorbic acid and flavonoids in onion, and flavonoids in garlic. The highest bulb concentrations of P and K were recorded under the AMF + Se application, Ca was best affected by AMF, and Mg accumulation was highest under all the treatments in garlic and upon AMF + Se application in onion bulbs. Contrary to garlic, onion bulbs were characterized by a remarkable increase in microelements (B, Cu, Fe, Mn, Si, Zn) under the AMF + Se treatment. Selenium, either with or without AMF application, promoted the accumulation of B and Si in onion and Mo and Zn in garlic bulbs. It can be inferred that the interaction between AMF and Se is highly specific, differing for garlic and onion grown in similar environmental conditions in Grozny region, Chechen Republic.