Animals breeding in nest-boxes experience nesting environments in which they did not originally evolve. Despite the central importance of nesting microclimate for offspring fitness, little is known about the thermal properties of human-provided nest sites compared to natural ones. In particular, comparisons with offspring in the nest are lacking. Here, we compare microclimate (temperature and absolute humidity) from the onset of breeding, thus starting with nest-site choice and ending with the post-fledging stage, quantified in natural cavities and nest-boxes used by several species of hollow-nesting birds in a temperate deciduous forest. We confirm that across all nesting stages, nest-boxes were thermally unstable when compared to natural cavities, with higher temperature maximums, larger amplitudes and worse insulation from maximum ambient temperatures relative to natural cavities. Surprisingly, as average humidity of natural cavities was previously shown to be higher than in nest-boxes, in the presence of actively thermoregulating young, nest-boxes were more humid than natural cavities. When offspring were in the nest, internal microclimatic shifts were mitigated three times more effectively in natural cavities than in nest-boxes (in terms of mean daily differences from ambient temperature). Artificial cavity microclimate is likely to amplify the adverse effects of projected temperature increases by compromising thermoregulation of developing animals. We stress that conservation efforts should focus on the protection of areas offering natural breeding-hollows to reduce the potential impacts of climate change on breeding animals.