On 27 January 1537, the Bernese occupiers secularised the monastery in Romainmôtier. The abbey church became a Protestant place of worship, and was gradually demolished and transformed. The twelve remaining monks had to choose whether to convert or go into exile.
The Prior’s House became the official residence of the bailiff appointed by Bern between 1537 and 1798. The other buildings were let, sold, or transformed into cellars or grain stores. Romainmôtier became the capital of a very profitable bailiwick on account of its seigneurial rights and the volume of its tithes. In 1798, following the revolution in Vaud, its territory was divided between the districts of Orbe, Cossonay, la Vallée de Joux, Aubonne and Rolle. The majestic lime tree behind the church was planted to celebrate the end of Bernese rule.