Purpose Exclusive breastfeeding promotes gut microbial compositions associated with lower rates of metabolic and autoimmune diseases. Its cessation is implicated in increased microbiome-metabolome discordance, suggesting a vulnerability to dietary changes. Formula supplementation is common within our low-income, ethnic-minority community. We studied exclusively breastfed (EBF) neonates’ early microbiome-metabolome coupling in efforts to build foundational knowledge needed to target this inequality. Methods Maternal surveys and stool samples from seven EBF neonates at first transitional stool (0–24 hours), discharge (30–48 hours), and at first appointment (days 3–5) were collected. Survey included demographics, feeding method, medications, medical history and tobacco and alcohol use. Stool samples were processed for 16S rRNA gene sequencing and lipid analysis by gas chromatography-mass spectrometry. Alpha and beta diversity analyses and Procrustes randomization for associations were carried out. Results Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were the most abundant taxa. Variation in microbiome composition was greater between individuals than within ( p =0.001). Palmitic, oleic, stearic, and linoleic acids were the most abundant lipids. Variation in lipid composition was greater between individuals than within ( p =0.040). Multivariate composition of the metabolome, but not microbiome, correlated with time ( p =0.030). Total lipids, saturated lipids, and unsaturated lipids concentrations increased over time ( p =0.012, p =0.008, p =0.023). Alpha diversity did not correlate with time ( p =0.403). Microbiome composition was not associated with each samples’ metabolome ( p =0.450). Conclusion Neonate gut microbiomes were unique to each neonate; respective metabolome profiles demonstrated generalizable temporal developments. The overall variability suggests potential interplay between influences including maternal breastmilk composition, amount consumed and living environment.