Many birds initiate incubation before clutch completion, which results in asynchronous hatching. The ensuing within–brood size disparity often places later–hatched nestlings at a developmental disadvantage, but the functional significance of the timing of the onset of incubation is poorly understood. Early incubation may serve to maintain the viability of early–laid eggs, which declines over time owing to the putative effects of ambient temperature. An unexplored risk to egg viability is trans–shell infection by micro–organisms. We experimentally investigated the rate and magnitude of microbial trans–shell infection of the egg, and the relative effects of ambient temperature and micro–organisms on hatching success. We show that infection of egg contents is prevalent and occurs within the time required to lay a clutch. The probability of infection depends on the climatic conditions, the exposure period and the phylogenetic composition of the eggshell microbiota. We also demonstrate that microbial infection and ambient temperature act independently to reduce egg viability considerably. Our results suggest that these two factors could affect the onset of avian incubation in a wide range of environments.