A cross-sectional study was carried out to determine the prevalence of pathogenic zoonotic agents (flaviviruses, avian influenza viruses (AIVs), Salmonella spp. and Toxoplasma gondii) in feral pigeons and sympatric zoo animals from Cordoba (Southern Spain) between 2013 and 2014. Antibodies against flaviviruses were detected in 7.8% out of 142 (CI95%: 3.7-11.8) pigeons, and 8.2% of 49 (CI95%: 0.9-15.4) of zoo animals tested. Antibodies with specificity against West Nile virus (WNV) and Usutu virus (USUV) were confirmed both in pigeons and in zoo birds. Even though seropositivity to AIVs was not detected in any of the analyzed pigeons, 17.9% of 28 (CI95%: 3.7-32.0) zoo birds tested showed positive results. Salmonella spp. was not isolated in any of 152 fecal samples collected from pigeons, while 6.8% of 44 zoo animals were positive. Antibodies against T. gondii were found in 9.2% of 142 (CI95%: 4.8-13.6) feral pigeons and 26.9% of 108 (CI95%: 19.6-34.1) zoo animals. This is the first study on flaviviruses and T. gondii in feral pigeons and captive zoo species in Spain. Antibodies against WNV and USUV detected in non-migratory pigeons and captive zoo animals indicate local circulation of these emerging pathogens in the study area. T. gondii was widespread in species analyzed. This finding could be of importance for Public Health and Conservation of endangered species present in zoo parks. Pigeons and zoo animals may be included as sentinel species for monitoring zoonotic pathogens in urban areas.