AbstractUrbanization and the expansion of human activities foster radical ecosystem changes with cascading effects also involving host‐pathogen interactions. Urban pollinator insects face several stressors related to landscape and local scale features such as green habitat loss, fragmentation and availability reduction of floral resources with unpredictable effects on parasite transmission. Furthermore, beekeeping may contribute to the spread of parasites to wild pollinators by increasing the number of parasite hosts. Here we used DNA‐based diagnostics tools to evaluate how the occurrence of parasites, namely microsporidians (Nosemaspp.), trypanosomatids (Crithidiaspp.) and neogregarines (Apicystis bombi), is shaped by the above‐mentioned stressors in two bumblebee species (i.e.Bombus terrestrisandBombus pascuorum). Infection rates of the two species were different and generally higher inB. terrestris. Moreover, they showed different responses towards the same ecological variables, possibly due to differences in body size and foraging habits supposed to affect their susceptibility to parasite infection. The probability of infection was found to be reduced inB. pascuorumby green habitat fragmentation, while increased along with floral resource availability. Unexpectedly,B. terrestrishad a lower parasite richness nearby apiaries maybe due to the fact that parasites are prone to be transmitted among the most abundant species. Our finding supports the need to design proper conservation measures based on species‐specific knowledge, as suggested by the variation in the parasite occurrence of the two species. Moreover, conservation policies aiming at safeguarding pollinators through flower planting should consider the indirect effects of these measures for parasite transmission together with pollinator biodiversity issues.