There has been a dairy at Kragerup since the 15th century. The first larger dairy, built on the estate with significant sales in mind, was constructed in the 1840s. Shortly after, the dairy was expanded and modernized to increase the production of the whey cheese “myseost” intended for export. Later, other types of cheese such as Emmental were also produced. Kragerup's whey cheese was awarded a bronze medal at the dairy fair in Paris in 1865.

Today, mejeriet consists of hotel rooms on both the ground floor and the first floor.