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In many regions of the world, the production of vegetable crops is limited by a deepening water crisis. Drought stress affects productivity and the chemical composition of crops. The variability of drought tolerance between species and cultivars of economically important crops, such as pepper (<i>Capsicum</i> species), requires specific investigations to understand the physiological and biochemical responses to the aftermath of drought. The fruits and leaves of four chilli pepper cultivars were investigated to elucidate the fruits&#8217; pungency (Scoville Heat Units, SHU), ascorbic acid content, DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity, polyphenol content, membrane lipid peroxidation and key protective antioxidant enzyme activity under drought stress (18&#8722;28% volumetric water content) as compared to the control (35&#8722;60%). Drought increased the chilli pepper fruits&#8217; pungency expressed in Scoville Heat Units (SHU) as well as ascorbic acid content, but this relationship was also dependent on genotype and stress duration. &#8216;Jolokia&#8217; was marked as most sensitive to drought by increasing content of capsaicinoids and DPPH˙ scavenging activity under stress conditions. Capsaicinoids and Ascorbic acid (AsA) greatly influenced the antioxidant activity of highly pungent chilli pepper fruits, although total phenols played a significant role in the mildly pungent genotypes. Generally, the activities of antioxidant enzymes increased under drought in chilli pepper leaves and fruits, although the intensity of the reaction varied among the cultivars used in the current research. All the investigated biochemical parameters were involved in the drought response of chilli pepper plants, but their significance and effectiveness were highly cultivar-dependent.