Two fires, one in 1282 and one in 1294, destroyed a large part of the church and all of the monastic buildings. The subsequent reconstruction work marked the transition to a more modern style: Gothic.
The porch leading into the narthex, the sanctuary and the ribbed vaulting in the nave provide the best examples of this. The repairs carried out saw the addition of sumptuous ornamentation, paintings and richly decorated funerary monuments, notably those of Henry de Sévery and Jean de Seyssel, both of whom were priors at Romainmôtier.
Some of the changes gave the abbey a slightly different silhouette. In the 15th century, the monks modified the crossing tower by erecting a tall, slender spire known as a flèche on top.
It was also during this period that the imposing bulk of the prior’s residence and the towers in the surrounding walls were built. They can still be seen today (Prior’s House, Clocktower, St George’s Tower).