Simple SummaryMicroorganisms may have direct negative effects on their animal hosts and cause diseases, but some others provide animals with protection against infections, parasites, and even predators. However, parasites or predators might take their cue from odors produced by bacteria, even those from protecting microorganisms, which could turn net benefits of bacteria that are a priori considered beneficial into a neutral or even negative outcome. This possibility has scarcely been studied in wildlife populations; we manipulated the bacterial community of nest-material of hoopoes and detected a negative effect in terms of the intensity of parasitism by blood-sucking flies that nestlings suffer. We also detected a positive link between the bacterial density of the nest-materials and the intensity of ectoparasitism, which further points at the importance of the bacteria determining the level of parasitism. Blood-sucking ectoparasites are also disease vectors, affecting both humans and livestock, and considering the role of the bacterial environment might help to establish new transmission control protocols.Nest bacterial environment influences avian reproduction directly because it might include pathogenic- or antibiotic-producing bacteria or indirectly because predators or ectoparasites can use volatile compounds from nest bacterial metabolism to detect nests of their avian hosts. Hoopoes (Upupa epops) do not build nests. They rather reuse holes or nest-boxes that contain remains of nest-materials from previous breeding seasons. Interestingly, it has been recently described that the nest’s bacterial environment partly affects the uropygial gland microbiota of hoopoe females and eggshells. Blood-sucking ectoparasites use chemical cues to find host nests, so we experimentally tested the hypothetical effects of microorganisms inhabiting nest-material remains before reproduction regarding the intensity of ectoparasitism suffered by 8-day-old nestling hoopoes. In accordance with the hypothesis, nestlings hatched in nest-boxes with autoclaved nest-material remains from the previous reproductive seasons suffered less from ectoparasites than those hatched in the control nest-boxes with nonautoclaved nest-material. Moreover, we found a positive association between the bacterial density of nest-material during the nestling phase and ectoparasitism intensity that was only apparent in nest-boxes with autoclaved nest-material. However, contrary to our expectations, nest bacterial load was positively associated with fledgling success. These results suggest a link between the community of microorganisms of nest-material remains and the intensity of ectoparasitism, and, on the other hand, that the nest bacterial environment during reproduction is related to fledging success. Here, we discuss possible mechanisms explaining the experimental and correlative results, including the possibility that the experimental autoclaving of nest material affected the microbiota of females and nestlings’ secretion and/or nest volatiles that attracted ectoparasites, therefore indirectly affecting both the nest bacterial environment at the nestling stage and fledging success.