Metabolomics of faecal samples offers a non-invasive method to monitor gastrointestinal (GI) development and microbial activity in dairy heifers during key physiological transitions. In this longitudinal study, faecal metabolites from 10 Holstein heifers were analyzed from birth to first calving using targeted metabolomics. Faecal samples were collected at 12 h post-birth, week 6 (pre-weaning), week 14 (weaning), 8 months (post-weaning), and at first calving (26 ± 2.3 months). Calves were fed 3.8 L of colostrum within 2 h of birth, followed by 6 L of maternal transition milk for 5 days, then 6 L of milk replacer twice daily. Group housing began at 14 days. Partial least squares discriminant analysis (PLS-DA) showed distinct temporal clustering of faecal metabolites. Heatmap analysis revealed significant metabolite alterations, particularly between pre- and post-weaning stages. A linear mixed-effects model identified significant stage effects for all 17 amino acids. Of the 55 biogenic amines and amino acid-related metabolites, 48 significantly differed across stages. Elevated amino acids and polyamines early in life reflected colostrum intake and immature digestion, decreasing post-weaning, indicating improved nutrient absorption and rumen functionality. Increased microbiota-derived compounds, including β-alanine, serotonin, and indole derivatives, reflected microbial colonization and co-regulation with the host. Elevated dopamine, homocysteine, and phenylethylamine in late gestation indicated neuroactive and redox adaptations. Overall, faecal metabolite profiles provide insights into metabolic remodelling related to nutrition, GI maturation, and reproductive development, highlighting faecal metabolomics as a useful non-invasive tool for monitoring heifer development.