The predicate the Elder is sometimes used to distinguish him from his nephew, John the Younger, who held Sønderborg from 1564 as a partitioned-off duke.

As a possible heir to the throne, he enjoyed a careful education and spent several years at the court of his brother-in-law Albert, Duke of Prussia, in Königsberg.

His territory consisted of the Counties of Haderslev, including Tørning, Tønder, and Løgumkloster, and the islands of Nordstrand and Fehmarn in Schleswig, plus Rendsburg and some smaller communities in Holstein.

As one of the first rulers between the seas, he sat down for an active land reclamation and coastal protection program, presumably, he ruled over the most vulnerable stretch of the Schleswig coastline.

In 1559, John, his brother Adolf, and King Christian's successor, Frederick II of Denmark, occupied the independent peasant Republic of Dithmarschen, and divided it among themselves.