Lesser Kestrel Falco naumanni (Fleischer, 1818) populations have been one of the best monitored bird populations in Spain over the last 70 years. These populations suffered a sharp decline between the 1950s and 1990s. Since then, periodic censuses showed a population increase that lasted until the 2010s. In those years, numerous projects for the recovery of the species were also initiated (some EU LIFE Projects, among others), which have continued to the present day. However, despite conservation efforts, the Spanish Lesser Kestrel population, which includes about 40% of the European breeding population, has declined at a rate of 6% per year since 2012. In this study, we analysed changes in habitat and population size in 12 colonies located in La Mancha between 2003 and 2021 in order to identify possible causes of the current decline. This colonial species breeds in old buildings, and roof area (a proxy for house size) was the predictor that best accounted for the number of pairs in a colony in a given year. In addition, the extent of herbaceous crops (related to prey availability) explained a similar amount of colony size variance in 2021, whereas in 2003, the availability of large Orthoptera itself had a significant effect but a much lower effect size. The number of nestboxes affected positively the number of breeding pairs in 2021 but explained only 1% of the variance. The decline of the Lesser Kestrel population between 2003 and 2021 was largely explained by the decrease of the density of large orthopterans, their main prey. The model with the minimum Akaike Information criterion adjusted for small sample size (AICc) value also included a positive association with changes in roof area and a negative association with rabbit density (possibly through a hyperpredation phenomenon). Other top models (i.e. ΔAICc ≤ 2 units) also showed negative effects of the loss of favourable land uses (pasture lands and herbaceous crops) on colony size, probably because this caused a reduction in the availability of large Orthoptera. These changes in land use occurred less often in areas protected by the Natura 2000 network, which may thus have contributed to the conservation of the Lesser Kestrel population. However, other conservation measures such as the installation of nestboxes were not as efficient as expected.