Urbanization is a significant source of inter- and intra-city environmental variation and is associated with declining population sizes that are increasingly homogeneous. However, whether this shift extends to urban disease ecology and related parasite communities, requires further examination. By comparing the prevalence and diversity of two related parasite genera (host-generalist Plasmodium and host-specialist Haemoproteus) in dark-eyed junco (Junco hyemalis) populations across an urbanization gradient in California, we can determine how broad urban-associated land use changes and localized habitat composition correlate with pathogen communities. Additionally, by examining vector abundance responses, we can begin to assess broader impacts on urban disease transmission and ecology. We report Haemoproteus prevalence decreased in urban habitats, with a larger presence of host-generalist lineages, suggesting urbanization increases homogenization of host-specialist pathogens. Unsurprisingly, the host-generalist pathogen, Plasmodium, showed no correlation with urbanization but prevalence increased with rainfall. Local habitat characteristics had limited effects on Plasmodium infection prevalence, but moderate shrub coverage and low human presence were associated with Plasmodium infections. Lastly, Culex tarsalis, an important vector for Plasmodium and zoonotic diseases, was the only vector to also increase in abundance in response to rainfall. Our results show that broad land use changes associated with urbanization decrease avian parasite biodiversity and highlight localized abiotic and biotic habitat characteristics that may reduce infection prevalence.