Veterinary tetracyclines drugs are emerging organic pollutants detected at high concentrations in the urine of school children and a potential public health risk. However, the implications of early-life exposure to tetracyclines on testosterone production, being new endocrine disruptors, remain unknown. We investigated whether the early-life exposure to low-doxycycline, a widely used tetracycline, on mitochondria dysfunction and testosterone disruption in Leydig cells in vitro and in vivo. Next, we determined the mRNA levels of testis cells markers for early-life exposure to low-doxycycline outcomes of testis health in later-life. Finally, we compared the weight gain performance exposed to low- and therapeutic-doses through 15 weeks and examined the role of the microbiota during development. Our results showed doxycycline disturbed steroidogenesis process by mitochondrial dysfunction in mouse Leydig tumor cell line (MLTC-1) cells in vitro. Leydig cells mitochondrial function was disrupted by early-life exposure to low-doxycycline from birth to 49 days, causing testosterone deficiency and decreased quality of the sperm in mice. Early-life exposure to low-doxycycline significantly altered the mRNA levels of key genes in Leydig cells (Cyp11a1, Cyp17a1 and 17β-HSD) and spermatogenic cells (Grfal, Plzf, and Stra8) in later-life in mice. Subchronic low- and therapeutic-doses doxycycline changed gut microbiota differences in diversity reduction and compositional alteration. Moreover, the weight gain effects of doxycycline were only observed in low-dose in male mice. Overall, these results provide insight into the effects of doxycycline on both testis and gut microbiota health. The results provide insight that environmental antibiotics are needed additional research to classify as ECDs.