Modernization of urban buildings can decrease the availability of nesting sites in buildings, leading to sudden decreases in the density of avifauna. In this study, we investigated the use of nest boxes as a bird conservation measure after buildings were thermally modernized. In a 10 ha experimental area we mounted five types of nest boxes of different sizes and dimensions (a total of 132). Nest boxes were dedicated to species that lost access to their previous nesting sites. All species associated with the buildings significantly declined or disappeared. In the first year after the modernization, the House Sparrow (Passer domesticus) decreased by 66% compared with the period before the modernization, Eurasian Jackdaw (Corvus monedula) by 68%, Common Starling (Sturnus vulgaris) by 70%, and Common Swift (Apus apus) by 100%. In the first two years after the modernization, the birds nested only in nest boxes. Five years of monitoring showed that using nest boxes as compensation for bird nesting sites lost during the renovation of buildings can cause a population to recover to ca. 50% of its original level. To optimize deployments of nest boxes, wildlife managers should consider target species’ preferences for the dimensions and placement of boxes and limit the time boxes are used if a species prefers nesting outside nest-boxes, but in buildings (e. g. the House Sparrow) and does not require additional support.