Agricultural intensification represents one of the major drivers for the dramatic loss of biodiversity worldwide. To halt the decline of farmland biodiversity, Switzerland adopted agri-environment schemes (AES) in 1998. Here, we monitored the occurrence, abundance and habitats of two species of arable bryophyte specialists, the Field hornwort (Anthoceros agrestis) and the Carolina hornwort (Phaeoceros carolinianus), in 28 crop fields in the intensively cultivated Swiss Plateau from 1991–2018, to investigate the effects of arable management, AES directives, and weather conditions on their performance. The target species are characteristic of the specialized short-lived arable bryophyte flora of Central Europe that depend on bare substrate in low-intensively cultivated and regularly ploughed fields. Trends in their occurrence thus reflect in many respects the status of the arable bryophytes in cultivated fields. Hornwort occurrence significantly declined between 1991 and 2018. A strong decrease in stubble fields that remain unmanaged after harvest, the favourite habitat for many arable specialists in the study area, largely accounted for the decline. Stubble fields nearly disappeared in the study area because of a gradual reduction in the cultivation area of cereals and the increasing practice of immediate post-harvest tillage. The latter is common in intensive arable farming and was accentuated by AES directives amended in 2005. Hornwort occurrences were positively affected by high air humidity during summer, but weather effects were subordinate to management effects. We propose tailored amendments of AES regulations, that aremented at selected sites, to maintain the characteristic arable specialist bryophytes in the Swiss Plateau: crop rotation with adequate proportions of cereals that are regularly ploughed but not before the end of October, no post-harvest processing of stubble fields, and optimization of the existing instrument ‘Biodiversity Promoting Areas’, e.g., short-term fallows in crop fields. Late-autumn or overwintering stubbles and short-term fallows will benefit many other organisms that depend on extensively managed open habitats, for example arableflowers, farmland breeding birds and specialized arthropods