Background Intensifying food production systems underscore the need for poultry gut-health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, vital for nutrient absorption, immunity, and disease resilience. Results We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to characterise caecal responses of commercial broilers to two widely used gut health interventions: ionophore supplementation (T1) and Eimeria vaccination (T2). Across 7,554 detected metabolites, interventions produced distinct metabolic ecologies. T1 was marked by prenol lipids, including multiple soyasaponins, and enrichment of cellular stress related pathways (e.g. glutathione pathway). T2 instead shifted aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. Integration with metagenomic profiles revealed complete discrimination between treatments and identified 405 metabolite-MAG correlations. Bacteroides fragilis emerged as a key metabolic influencer, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis linked Mediterraneibacter spp. to soyasaponin deglycosylation via glycosidase and rhamnosidase genes, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps. Conclusion Our findings reveal that prophylactic interventions distinctly modulate gut microbial functions, shaping metabolic outcomes. Our study highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut-health centred approaches in both veterinary and human contexts.