Species’ distribution models are widely used in landscape ecology but usually lack explicit information about species’ responses to ecosystem dynamics, leading to uncertainty when applied to the prediction of seasonal change in distributions. In this study, we aimed to build a species’ distribution model for the Common Quail Coturnix coturnix, a farmland species that shows changes in its distribution in response to seasonal changes in habitat suitability. During the course of three breeding seasons we collected temporal replicates of presence–absence data in 13 sampling locations in four countries (Morocco, Portugal, Spain and France). We used generalized linear mixed models to relate the species’ presence or absence to environmental variables and to the normalized difference vegetation index at each sampling location through the seasons, the latter variable being an indicator of within- and between-season habitat changes. The preferred model showed that occurrence was highly dependent on habitat changes associated with crop seasonality, as measured by the normalized difference vegetation index. Common Quail selected areas with dense vegetation and warm climate and tracked spatial changes in these two parameters. The model allows accurate mapping of within- and between-season distribution changes. Such changes are related to habitat variations caused mainly by drought and agricultural practices. Our results demonstrate that seasonal changes in farmland ecosystems can be incorporated into a simple distribution model, and our approach could be applied to other species to predict the effects of agricultural changes on the distribution of birds inhabiting farmland landscapes.