This study aimed to evaluate the prevalence, taxonomic diversity, co-infection patterns, and outcomes of routine prophylactic practices for gastrointestinal parasites in avian and mammalian species housed in a zoo in Ankara. A total of 272 fresh fecal samples were collected and examined using flotation and sedimentation techniques. Associations with class and sex were analyzed using Chi-square/Fisher’s exact tests and logistic regression. The overall positivity rate was 30.5% (95% CI: 25.3–36.2); 35.1% in birds (95% CI: 27.9–43.1) and 25.0% in mammals (95% CI: 18.2–33.3). However, the effect of class was not confirmed in the multivariable model. The most frequent taxon was Eimeria spp. (15.4%), while strongylid-type eggs, Capillaria spp., Ascaridia spp., and Nematodirus spp. were detected at lower rates. Co-infections were common, with Eimeria spp. occupying a central position within the network. Routine antiparasitic treatments yielded marked benefits against nematode targets, with fecal negativity reaching 83.5% in treated animals, 82.9% with ivermectin, and 100% with selamectin in a small sample. Nevertheless, Eimeria burden persisted, highlighting the need for concurrent anticoccidial treatment and environmental interventions such as litter and moisture control. The findings support the critical importance of regular fecal parasitological surveillance tailored to taxonomic class and species, along with combination prophylaxis, for welfare improvement and infection control in zoo settings.