The Agave potatorum Zucc. is a wild species endemic to Oaxaca and Puebla, Mexico. The stem or “head” of the plants of this species contains a large amount of fructans, which, in conjunction with their crassulacean acid metabolism (CAM), helps the agave to survive droughts. The soluble carbohydrates are used to produce mezcal. The objective was to evaluate growth and content of fructans of A. potatorum young plants grown in soil and perlite substrate, fertigated with three nutrient solutions, and subjected to drought. Eight-month-old plants were used and, for 15 months, were fertigated with nutrient solutions: 1) Steiner, 2) Hoagland and Arnon, and 3) Urrestarazu. Irrigation was later suspended to simulate a 5-month drought and induce stress. During fertigation, the vegetative growth was greater in plants irrigated with Hoagland and Arnon and Urrestarazu solutions in perlite and in soil. After the period of water deficit stress, plants in perlite substrate fertigated with the Hoagland and Arnon solution accumulated more fructans in the heads, reaching a maximum of 75%, than plants in soil substrate (42%).