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Water stress negatively impacts the physiology of plants, affecting their growth and development. It is considered among the most important environmental factors responsible for reduced crop production. In this regard, biofertilizers may be considered significant for their reparative properties to increase stress tolerance in crop plants. We studied the effects of water stress on the morphological and biochemical characteristics of onion plants with AMF (<i>Funneliformis mosseae</i>) and potassium silicate application. The water stress significantly affected all the studied traits, each with minimum recorded levels. Plants that received combined treatments of AMF and potassium silicate showed maximum percent increments in all the studied characteristics, e.g., plant height (156.7%), weight of bulb (416.8%), antioxidant activity (224.0%), membrane stability index (74.5%), relative water content (87.3%), and total soluble solids (63.71%). Therefore, the study demonstrated that all the investigated variables were affected negatively by water stress. However, bio-fortification of onion plants with silicates and AMF inoculation may be considered useful for functional food production, with numerous health promoting properties.