Invasive plant pathogens have impacted forest and woodland systems globally and can negatively impact biodiversity. The soil-borne plant pathogen Phytophthora cinnamomi is listed as one of the world's worst invasive species and alters plant community composition and habitat structure. Few studies have examined how these Phytophthora-induced habitat changes affect faunal communities. We examined bird communities in Banksia woodland with, and without, Phytophthora dieback in a biodiversity hotspot, southwestern Australia. Seven sites along dieback fronts, with paired 1-ha plots in diseased and healthy vegetation, were surveyed monthly for birds over seven months. Vegetation assessments showed that diseased sites had reduced plant species richness, litter, shrub, tree and canopy cover, high bare ground and significantly lower flowering scores, than healthy sites. Bird community composition differed significantly between diseased and healthy sites, although total bird abundance, total species richness and foraging guilds, did not. Average species richness of birds per survey and the abundance of brown honeyeaters, western spinebills and silvereyes was lower in diseased than healthy sites. The tawny-crowned honeyeater had higher abundances in diseased sites. Similarity matrices of habitat structure, flowering scores and bird assemblages were congruent, indicating that habitat structural differences were influencing bird community composition. Our results suggest that this pathogen is potentially a serious threat to avian biodiversity and especially for nectarivores, and populations in fragmented landscapes. Since elimination of the pathogen is not currently possible, management should focus on methods of preventing its spread until techniques to eliminate the pathogen are developed.