The Pühalepa Church is Hiiumaa’s oldest stone church. In 1255, the German Order started the construction of a stone fortress-church. Initially lacking a steeple, the arched stone church was completed in the 14th century; construction of the steeple started in 1770. After it renovation in the 19th century, Crosses of Malta were painted on the walls that are primarily associated with the membership of the Ungern-Sternberg family members in this Order.
One of the inauguration crosses has survived on the wall of the choir room.
An unusual stone pulpit was given to the Pühalepa Church by the Hiiesaare manor lords, the Gentschiens in 1636.
The burial chapel of the von Stenbock family is in the churchyard.