Obesity, particularly in infants, is becoming a significant public health problem that has reached “epidemic” status worldwide. Obese children have an increased risk of developing obesity-related diseases, such as metabolic syndromes and diabetes, as well as increased risk of mortality and adverse health outcomes later in life. Experimental data show that maternal obesity has negative effects on the offspring's health in the short and long term. Increasing evidence suggests a key role for microbiota in host metabolism and energy harvest, providing novel tools for obesity prevention and management. The maternal environment, including nutrition and microbes, influences the likelihood of developing childhood diseases, which may persist and be exacerbated in adulthood. Maternal obesity and weight gain also influence microbiota composition and activity during pregnancy and lactation. They affect microbial diversity in the gut and breast milk. Such microbial changes may be transferred to the offspring during delivery and also during lactation, affecting infant microbial colonisation and immune system maturation. Thus, an adequate nutritional and microbial environment during the peri-natal period may provide a window of opportunity to reduce the risk of obesity and overweight in our infants using targeted strategies aimed at modulating the microbiota during early life.