Ebeltoft Kirke is first mentioned in 1458, however, at this point in time, it is merely referred to as a chapel.
However, during an archaeological examination, that took place in connection with the restoration in 1983, coins dating to the 13th century were found, as well as foundational remains under the eastern part of the church, which show that even before the town in 1301 got market town rights, there was a smaller church.
Around the year 1500, the church was expanded to the current longhouse, with the addition of the five vaults and the tower with crenellated gables.
In the 16th century, the church had a woman's door to the north and a man's door to the south. On the south side, there was at one time a porch in connection with the entrance. However, the porch was torn down in the late 18th century.
In 2015, the church interior was restored, to which the church was given a different colour scheme which makes the church that stands today appear brighter, more harmonious and more distinctive.