This study examined the association between intestinal lactobacilli and obesity dependent on dietary patterns in children. A cross-sectional study was conducted including 1111 children, 6–12 years old. Obesity was determined according to the WHO cut-off points. Diet information from a Food Frequency Questionnaire identified three dietary patterns. Lactobacillus sp. were determined by a real-time polymerase chain reaction (PCR). The consumption of complex carbohydrates and a high abundance of L. paracasei were associated with a lower risk of obesity (0.35, Confidence Interval 95% 0.19–0.65). The same happened with a medium consumption of fats and a medium abundance of L. paracasei (0.43, CI95% 0.24–0.78). In contrast, an increased risk of obesity is observed with a medium and high consumption of simple carbohydrates (2.37, CI95% 1.29–4.34 and 2.52, CI95% 1.36–4.66, respectively, p-trend<0.05), and low consumption of complex carbohydrates (2.49, CI95% 1.35–4.58), in the presence of a high relative abundance of L. reuteri. A high relative abundance of L. paracasei decreased the risk of obesity, even when high-fat and simple carbohydrate diets were consumed; while a high relative abundance of L. reuteri was associated with a greater possibility of obesity with these types of diets. Our results provide evidence of diet implication in metabolism regulators like lactobacilli. This is helpful in strategies development to promote healthy diets during early stages of life.