The islet has served as a place of execution, a monastery, a fortress, a prison, and a World War II anti-aircraft gun station.

[2] In the years prior to the founding of the city of Trondheim in 997 by King Olav Tryggvason, Munkholmen had been used as an execution site by the Jarls of Lade.

The arrival of Olav Tryggvason to Norway in 995 coincided with a revolt against Haakon Sigurdsson, who was killed by Tormod Kark.

The severed heads of both Haakon and Kark were placed on stakes on Munkholmen facing out into the fjord to serve as a warning to visitors.

In the early 12th century, and possibly even earlier, Benedictine monks lived on the island in Nidarholm Abbey.

After capturing Trondheim early on in the Norwegian Campaign, the Germans quickly established a submarine base, exploiting the natural protection provided by the fjord.