Changes in climate have intensified the drought in semi-arid regions. A shift toward cultivation of low-input crops, including high-value medicinal and herbal plants seems a more sustainable alternative strategy. A 2-year field study was conducted to investigate the influence of drought stress and chitosan on nutrient density and phenolic compounds of thyme. Treatments consisted of a factorial combination of three irrigation and three chitosan rates. Irrigation treatments consisted of keeping experimental plots at field capacity (no stress), irrigation when plots reached 50% of field capacity (mild stress), and irrigation when plots reached 25% of field capacity (severe stress). Chitosan rates were 0, 200, and 400 μL L −1 , while K + , and to some degree Ca +2 , accumulation increased by drought, N, P, and all micronutrients (Mn 2+ , Zn 2+ , Cu 2+ , and Fe 2+ ) decreased steadily as drought stress intensified. Drought stress reduced N and P by 23%-19% and 35%-23%, respectively, over the 2 years. Application of chitosan enhanced the accumulation of macro and micronutrients. Drought stress resulted in alterations in phenolic composition. In mature plants, almost all phenolic compounds, except thymol, increased as drought stress intensified. Cinnamic acid and rosmarinic contents, as the two major identified compounds, increased by 31% and 45%, respectively, under severe drought. Similar to drought, chitosan elicitation was more effective in elevating phenolic compounds in mature plants. The response of thyme to chitosan was independent of soil moisture availability. The results indicated that application of 400 μL −1 chitosan improved nutrient density and dry matter while significantly saved irrigation water.