Toxoplasmosis affects a third of the global population and is of particular concern for immunologically compromised individuals. Toxoplasmosis induces host physiological events ranging from immunological to metabolic responses across multiple biological compartments. To understand the sequence of host responses during acute and chronic Toxoplasma gondii infection, eight male BALB/c mice were infected with 2000 T. gondii ME49 tachyzoites with a further eight uninfected mice used as controls. Plasma cytokines status, urinary metabolic profiling and fecal microbial profiles were characterized to monitor temporal variation related to T. gondii infection. The results showed elevated serum interferon-γ (IFN-γ), interleukin-12p40 and necrosis factor-α during acute phase of infection with concomitant perturbation in host energy metabolism and host-gut microbiome co-metabolism of phenolics and a shift in microbial composition. However, the differences were less pronounced during the putative chronic phase of infection with elevated IFN-γ, differences in urinary N-acetyls and O-acetyls of glycoproteins with no shift in gut microbial composition. Structural equation modelling on the current data showed host immune responses as the main driver for changes observed in urinary metabolites and gut microbial composition. Such an approach can be applied to other models of infectious diseases to aid understanding of host–pathogen interactions and potential biomarker discovery.