Introduction: This study investigates the effects of maternal obesity on microbiota composition and metabolite profiles in neonates and breast milk. Maternal obesity can alter the bacterial landscape and bioactive compounds in breast milk, increasing the risk of obesity in infants. The microbiota and metabolites in breast milk and neonatal fecal samples from obese and normal-weight Mexican mothers were compared. Methodology: Fecal and milk samples were collected from binomials. DNA extraction was performed, followed by the PCR amplification of the V3-16S ribosomal RNA gene for next-generation sequencing (NGS) analysis. Taxonomic microbiota profiling was conducted, and metabolic pathway analysis was carried out using PICRUST to identify pathways associated with different bacterial taxa. Metabolites were extracted and analyzed via FT-ICR mass spectrometry. Comprehensive bioinformatics analyses were conducted to assign taxonomy and assess bacterial diversity. Results: The findings suggest that the vertical transmission of bacteria and metabolites from mother to infant exists. Patescibacteria and Firmicutes were identified as dominant phyla in human milk. Fecal samples from neonates born to obese mothers exhibited a lower abundance of Bifidobacterium and Lactobacillus than those born to normal-weight mothers. In addition, fecal samples from neonates and milk from obese mothers were characterized by an increased abundance of Lactobacillus and Staphylococcus. Conclusion: This study highlights breastfeeding's crucial role in transferring maternal microbiota and metabolites to infants, showing strong microbial and metabolic connections between breast milk and meconium. Maternal BMI does not affect overall bacterial composition, but distinct metabolites linked to maternal obesity were found, suggesting potential neonatal health impacts. The research suggests a pathway for intergenerational obesity risk transmission via breastfeeding, emphasizing the need for further investigation into the long-term health effects on infants of obese mothers. This work was financed by CONACyT 163235 INFR-2011-01 and CONACyT FORDECYT-PRONACES/6669/2020_Programa Presupuestario F003-Ciencia de frontera 2019.