Large declines of farmland bird species have been observed in the lowlands of Western Europe, whereas important populations of some of these species have survived in parts of Eastern and Southern Europe and in small areas within Western Europe, e.g. in parts of the Alps. However, such extant hotspots of farmland biodiversity are at risk: The economic and technical developments threaten to erode biodiversity in existing hotspots, potentially repeating the collapse previously observed in Western Europe. We here present changes in the abundance of farmland birds in the Engadin in the Swiss Alps. Farmland birds such as Whinchat Saxicola rubetra and Skylark Alauda arvensis were still numerous in 1987/1988 when we first censused the area. During our second census period in 2009/2010, we noticed strong declines of such open country species, while several hedge and tree breeders as well as some species preferring warmer climate increased. We observed a good correlation between the change in the vegetation and in the birds. Both these changes were especially pronounced in areas with a recent agricultural improvement project. Thus, we believe that the change in farmland practices, which affected our mountainous study area much later than the lowlands, and possibly climate change, have led to a profound change in the regional avifauna. Using our data as a case study, we argue that similar, and similarly fast, changes may be on-going or imminent in many other areas with extant important populations of farmland species such as Whinchat and Skylark. Thus, our data add to the repeatedly declared urgency to adjust the advancement of agricultural subsidy systems to better accommodate biodiversity considerations, both in depauperated areas as well as in extant hotspots.