This study investigates the long-term metabolic consequences of altering the intestinal microbiota during a critical developmental window. Low-dose penicillin (LDP) exposure from birth transiently disrupts the microbiota, leading to sustained effects on body composition. LDP exposure at early life, either through maternal consumption or direct administration to pups, increases fat mass and bone mineral content in male mice, with more pronounced effects in males. The altered microbiota, not the antibiotics themselves, is responsible for these metabolic phenotypes. LDP enhances the effects of a high-fat diet, and the altered microbiota alone is sufficient to induce metabolic changes. The study identifies specific microbial taxa, such as *Lactobacillus*, *Allobaculum*, Rikenellaceae, and *Candidatus Arthromitus*, that are underrepresented in LDP-exposed mice and may play a protective role against weight gain. These findings highlight the importance of early-life microbiota in long-term metabolic programming and suggest that restoring lost taxa could potentially reverse microbe-induced obesity.This study investigates the long-term metabolic consequences of altering the intestinal microbiota during a critical developmental window. Low-dose penicillin (LDP) exposure from birth transiently disrupts the microbiota, leading to sustained effects on body composition. LDP exposure at early life, either through maternal consumption or direct administration to pups, increases fat mass and bone mineral content in male mice, with more pronounced effects in males. The altered microbiota, not the antibiotics themselves, is responsible for these metabolic phenotypes. LDP enhances the effects of a high-fat diet, and the altered microbiota alone is sufficient to induce metabolic changes. The study identifies specific microbial taxa, such as *Lactobacillus*, *Allobaculum*, Rikenellaceae, and *Candidatus Arthromitus*, that are underrepresented in LDP-exposed mice and may play a protective role against weight gain. These findings highlight the importance of early-life microbiota in long-term metabolic programming and suggest that restoring lost taxa could potentially reverse microbe-induced obesity.