Plant-based diets have been linked to various health benefits, including an improved gut microbiota composition, potentially influencing non-communicable diseases. This study investigates the impact of a school meal intervention on the gut microbiota, specifically the abundance of Bifidobacterium spp. (BIF), in Brazilian schoolchildren. A quasi-experimental intervention was conducted in 2019 across four municipalities in the semi-arid region of Bahia, Brazil. The Sustainable School Program aimed to replace animal-based and ultra-processed foods with plant-based options. Clinical, dietary, anthropometric, and laboratory data were collected at the beginning and end of the school year. Fecal samples were analyzed for BIF abundance using RT-PCR. The intervention improved anthropometric and laboratory outcomes, including increased serum hemoglobin levels and reduced LDL-cholesterol. Despite these benefits, no significant change in BIF abundance was observed. However, a negative correlation between BIF abundance and waist-to-height ratio was found. While the intervention positively affected several health parameters, it did not significantly alter BIF abundance. Nevertheless, the abundance of BIF may explain some of these positive outcomes. The findings highlight the potential of plant-based diets to improve overall health, but suggest that further research is needed to understand the role of the gut microbiota in these outcomes. Future studies should explore the influence of factors such as physical activity on the gut microbiota and health.