Drought is one of the major environmental stresses that impairs fruit productivity and quality. The proper management of minerals can, however, assist plant to maintain their growth even under drought incidents, and is considered one of the encouraging approaches to refine the drought tolerance of plants. The beneficial effects of chitosan (CH)-based Schiff base-metal complexes (e.g., CH–Fe, CH–Cu and CH–Zn) in reducing the harmful impacts of different levels of drought stress on the growth and productivity of ‘Malase Saveh’ pomegranate cultivar were examined. All CH-metal complexes displayed favorable effects on the yield- and growth-related attributes of pomegranate trees cultivated under well-watered and different drought situations, with the best effects were observed with CH–Fe application. Specifically, leaves of CH–Fe-treated pomegranate plants showed higher concentrations of photosynthetic pigments [chlorophyll a (Chl a), Chl b, Chl a+b, and carotenoids by 28.0, 29.5, 28.6 and 85.7%, respectively] and microelements (Fe by 27.3%), along with increased levels of superoxide dismutase (by 35.3%) and ascorbate peroxidase (by 56.0%) enzymatic activities relative to those of CH–Fe-non-treated pomegranate plants under intense drought stress. CH–Fe-treated drought-stressed pomegranate leaves showed high increment of abscisic acid (by 25.1%) and indole-3-acetic acid (by 40.5%) relative to CH–Fe-non-treated pomegranates. The increased contents of total phenolics, ascorbic acid, total anthocyanins, and titratable acidity (by 24.3, 25.8, 9.3 and 30.9%, respectively) in the fruits of CH–Fe-treated drought-stressed pomegranates indicated the advantageousness of CH–Fe on the enhancement of fruit nutritional qualities. Collectively, our results prove the explicit functions of these complexes, particularly CH–Fe, in the control of drought-induced negative effects on pomegranate trees grown in semi-arid and dry areas.