Natural nest sites are important breeding resource in terms of population dynamics, especially in forest systems where nest trees limit populations or timber harvesting destroys nests. Nest structures usually have a long life and can be reused by breeding pairs across multiple breeding seasons, so studying their dynamics is of relevance for biodiversity conservation. In this study, we develop a dynamic model to evaluate nest site availability and its influence on the breeding settlement of a forest raptor community composed of booted eagle (Hieraaetus pennatus), common buzzard (Buteo buteo) and northern goshawk (Accipiter gentilis) in a Mediterranean forest ecosystem in southeast Spain. This model approach is also applied to analyse the influence of forestry practices on the dynamics of occupied nests for a simulated period (2010–2050). The simulated scenarios include unmanaged forest and timber harvesting practices of clearcuttings every ten years considering two factors: the age class of trees for clearcutting (40, 50, 60 and 70 years old) and the type of forest management (with or without nest protection). Our simulated results show that the number of breeding pairs is constant during the period without timber harvest, whereas breeding pairs gradually decrease in the scenario of clearcutting trees aged from 70 to 50-years without nest protection, and populations become extinct with the clearcutting of 40-year old trees. Considering the practice of clearcutting and nest protection, nest occupancy can reach the maximum number of occupied nests for the scenarios of cutting 70 and 60-year old trees, and maintain populations without extinction for the scenarios of cutting 40-year old trees. We conclude that nest sites (whether occupied or not) are key resources for increasing the occupancy of the forest raptor community and that nest protection measures buffer the effects of clearcuttings, thus preventing population extinction.