The Rhynonyssid mesostigmatic mite, Sternostoma tracheacolum, is a well-documented endoparasitic hematophagous arthropod of the respiratory tracts of multiple avian species, particularly Estrildid finches and canaries. In this retrospective study, 175 medical and 278 pathology records for the Gouldian finch (Chloebia gouldiae) population (N = 377) at the San Diego Zoo between 2013 and 2021 were analyzed to evaluate the effectiveness of ivermectin-based prophylaxis. A multivariable negative binomial regression model was constructed to evaluate the population effects of monthly treatments on morbidity or mortality associated with respiratory mites. While controlling for other factors in the model, the prophylactic treatment did not significantly reduce the monthly rate of mite-associated morbidity or mortality (IRR = 1.017, 95% CI: 0.997-1.036, P = 0.0759); however, low proportions of the population were prophylactically treated over time. Different factors were significant when separately evaluating adjusted associations with respiratory morbidity and mortality. The findings suggest increased rates of respiratory morbidity for each successive year of the study period (IRR = 1.180, 95% CI: 1.046–1.342, P = 0.0090) and increased rates of mite-associated mortality occurring annually between May and October (IRR = 1.697, 95% CI: 1.034–2.855, P = 0.0404) compared to the wet winter season. Our findings highlight the need to continually evaluate and optimize treatment regimens in zoological collections. Further investigations into this host-parasite relationship and potential treatments and preventive therapies are warranted.