It was owned by the Catholic Church, but at the Reformation in 1536 it came in possession of The Crown.
King Frederick II exchanged it for some other estates owned by Danish nobleman and diplomat Jørgen Ottesen Rosenkrantz (1523-1596).
Unfortunately Otto died early, after which Skaføgård became a dower house for Jørgen's wife, Dorthe Lange (1541-1613) and after her death passed to their surviving son Holger.
It was later extended, standing complete in 1607 with four wings, clearly influenced by the French and Italian Renaissance styles.
The castle interior was modernised in the 1740s in the Baroque style, at which time a large baroque garden was laid out, covering an area of 5 ha., with avenues of limetrees and hedgerows of beech.