Dogs are hosts of the protozoans Toxoplasma gondii, which causes an important public health disease, and Neospora caninum. Studies that have evaluated toxoplasmosis and neosporosis for prolonged periods in dog populations are rare. We analyzed infection by both parasites in a domestic dog population over three consecutive years in São Paulo state, Brazil. In the 1st, 2nd and 3rd years of collection, 181, 193 and 172 domiciles were visited, and blood samples of 331, 371 and 348 dogs were collected for antibody serology, respectively. The seroprevalence of T. gondii in each year was 27.2%, 22.5% and 43.9%, respectively, and that of N. caninum was 7.8%, 4.8% and 6.8%, respectively. The incidence rates for T. gondii in the 2nd and 3rd collections were 13.2% and 30.0%, and those for N. caninum were 3.3% and 4.4%, respectively. Positive and negative serological conversions for both agents occurred at high frequencies during the study period. This study reveals the canine population’s serological profile and demonstrates the constant exposure of dogs to the investigated pathogens, indicating the need for prevention and control measures in the region.