Abiotic stress, including drought, cold, high temperature and UV radiation, produce common responses in plant tissue, resulting in the overproduction of Reactive Oxygen Species (ROS). ROS molecules damage cell membranes and disrupt plant metabolism. Our previous experiments indicated that naturally chelated/complexed foliar nutritional supplement products reduce the amount of ROS molecules formed under stress conditions. In this study, we investigated the short-term effect of the novel proprietary biostimulant CYT31 on gene expression in plants exposed to drought using Arabidopsis thaliana grown under controlled conditions. Plants were sprayed with biostimulant CYT31 (treated) or water (control). One hour after spraying, plants were exposed to drought conditions for one, two or four hours. Tissue was collected for two-color microarray and cell damage analysis. Tissue damage was evaluated using an electrolyte leakage-detection method. Drought stress up-regulated over 245 genes involved in water deprivation, redox and stress response. The gene response was influenced by the severity of the stress and correlated with tissue damage. The up-regulation of these genes was significantly altered in the tissue treated with biostimulant CYT31, suggesting the activation of several mechanisms leading to the reduction of tissue injury. Gene activation was confirmed by quantitative polymerase chain reaction (qPCR) analysis. This paper describes a proposed model for metabolic pathways activated by biostimulant CYT31 in plants exposed to drought stress.