Background: The importance of prebiotics consumption is increasing all over the world due to their beneficial effects on health. Production of better prebiotics from endemic plants raises possibilities to enhance nutritional effects in vulnerable population groups. Fructans derived from Agave Plant have demonstrated their safety and efficacy as prebiotics in animal models. Recently, the safety in humans of two fructans obtained from Agave tequilana (Metlin and Metlos) was demonstrated. Methods: This study aimed to demonstrate the efficacy as prebiotics of Metlin and Metlos in newborns of a randomized, double blind, controlled trial with a pilot study design. Biological samples were taken at 20 ˘ 7 days, and three months of age from healthy babies. Outcomes of efficacy include impact on immune response, serum ferritin, C-reactive protein, bone metabolism, and gut bacteria changes. Results: There were differences statistically significant for the groups of infants fed only with infant formula and with formula enriched with Metlin and Metlos. Conclusions: Our results support the efficacy of Metlin and Metlos as prebiotics in humans, and stand the bases to recommend their consumption. Trial Registration: ClinicalTrials.gov, NCT 01251783.