In the High and Late Middle Ages, towers were added to the existing church; In the 14th and 15th centuries, the church, rectory, sacristan's house and some of the surrounding courtyards were completely rebuilt into a fortified church. From the first St. John's Church, only the foundation walls and a loophole that is now covered by the plaster are archaeologically detectable. During the second destruction of Ipsheim in the First Margrave War in 1449, the fortified church was probably destroyed, while it apparently survived the first conquest in 1388 without major damage.
In the course of the 15th century, with its numerous wars and feuds in the Ipsheim area, the church was rebuilt in the Gothic style. The fortified church was turned into a fortified church with four corner towers, which was intended as a last resort for the villagers in troubled times. A fireproof tower was built at the western portal; the Gaden were built together in such a way as to form a true fortification, which was supplemented in places by a ditch; storage rooms, emergency shelters, a fire pond and a defense tower were also installed. The rectory, cemetery wall and church chancel shielded the complex from the south and east, the school, the sacristan and the integrated courtyards from the north and west. In the church itself, the chancel was extended to the east and a side chapel was built under the small tower. In the 16th century, a property integrated into the fortified church was converted into a schoolhouse.