The Dutch Renaissance style main building was built in 1579 for Chancellor of the Realm Eiler Grubbe (1532–1585).

One of his sons, Jørgen Grubbe fell into captivity in Turkey and later settled in East Prussia.

He led a quiet life on his estate without offices at the court and did not marry until the age of 37.

His son, Peder Grubbe, who served in the Torstenson War (1643-1645), inherited Lystrup after his father.

A few years prior to his death, Tønne Grubbe had endowed Lystrup to Claus Bendix Beenfeldt who was married to Christine Cathrine Statlander, a niece of Grubbe's late wife.

After Christian Holmsted's early death in 1754, Anna Vilhelmine Beenfeldt married Niels Rosenkrantz von Holstein-Rathlou.

Christian Frederik von Holstein-Rathlou's son-in-law, Johan Caspar Mylius (1776-1852) purchased the estate in 1831.

After his death in 1857, Lystrup was passed on to his brother, Frederik Vilhelm de Mylius, who sold it.