Land-use changes including agricultural intensification are major drivers of biodiversity loss. As other countries, Switzerland introduced agri-environment schemes (AES) to counteract declining agro-biodiversity. Among numerous bryophytes of the agricultural landscape, arable bryophytes have adapted to recurrent tillage. They are short-lived above-ground, while their diaspores may build up a persistent diaspore bank in the soil. We monitored the field hornwort and the Carolina hornwort, characteristic species of the Central European arable bryophyte flora over a period of almost three decades, and studied effects of Biodiversity Promoting Areas (BPAS), a key element of Swiss AES, on arable bryophyte diversity. Hornwort occurrences strongly declined, and stubble-fields left unprocessed until late autumn, the favourite habitat of arable specialist bryophytes, nearly disappeared from 1991 to 2018. The loss of suitable habitats follows from decreased cereal cultivation and direct post-harvest management. Different BPA-fallows, designed to promote birds, flowering plants, or ecosystem services, harboured arable bryophyte specialists, but their richness decreased with fallow age. Diaspore banks contained arable bryophyte specialists not occurring above-ground and may serve as a reservoir during unsuitable cultivation. Targeted modifications of current AES, aiming to maintain habitats favourable for arable bryophytes, are necessary to safeguard the typical arable bryophytes in the Swiss arable landscape.