Chlamydiae are obligate intracellular bacterial pathogens that may cause genital pathology via induction of destructive host immune responses. Human-adapted Chlamydia trachomatis causes inflammatory disease in human hosts but is easily cleared in mice and mouse-adapted Chlamydia muridarum establishes a productive and pathogenic infection in murine hosts. While numerous anti-chlamydial host resistance factors have been discovered in mice and humans alike little is known about host factors promoting host fitness independent of host resistance. Here we show that interferon-inducible immunity-related GTPase M (Irgm) proteins function as such host factors ameliorating infection-associated sequalae in the murine female genital tract thus characterizing Irgm proteins as mediators of disease tolerance. Specifically we demonstrate that mice deficient for all three murine Irgm paralogs (pan-Irgm−/−) are defective for cell-autonomous immunity to C. trachomatis which correlates with an early and transient increase in bacterial burden and sustained hyperinflammation in vivo. In contrast upon infection of pan-Irgm−/− mice with C. muridarum bacterial burden is unaffected yet genital inflammation and scarring pathology are nonetheless increased demonstrating that Irgm proteins can promote host fitness without altering bacterial burden. Additionally pan-Irgm−/− mice display increased granulomatous inflammation in genital Chlamydia infection implicating Irgm proteins in the regulation of granuloma formation and maintenance. These findings demonstrate that Irgm proteins regulate pathogenic immune responses to Chlamydia infection in vivo establishing an effective infection model to examine the immunoregulatory functions and mechanisms of Irgm proteins.