Small mammals have been seldom used as indicators of biodiversity responses to environmental changes, probably because their long-term population trend in a given area is not easy to monitor. To assess the impact of agricultural intensification in a protected area of northern Italy, we compared the composition of its small mammal communities, as assessed in 1994-1995 and 2015-2016 by the analysis of owl pellets (N = 265 and 302, respectively), which provides an effective and affordable method for assessing changes in the diversity and structure of small mammal assemblages over time. We recorded a sharp reduction in the frequency of occurrence of shrews (Sorex spp. and Crocidura spp.), which were replaced by generalist/anthropophilic rats (Rattus norvegicus) and house mice (Mus domesticus). Overall richness and diversity of the community varied only slightly, while trophic level and functional diversity indices clearly reflected the decline of the predator-level fraction of the community. We could reliably exclude both broad-scale land use- and climate changes as drivers of variation in the composition of small mammal communities and ascribe the decline of insectivores to changes in agricultural practices, namely the increase in cover of maize fields and spread of both herbicides and insecticides. Our results are consistent with the general opinion that crop specialization and increasing chemical inputs reduce the diversity and abundance of invertebrate prey, with bottom-up effects on higher trophic levels.