Winstrup was born in Copenhagen – then part of the Denmark–Norway empire. He was the son of Peder Jensen Vinstrup, Bishop of Sjaelland and professor of theology at the University of Copenhagen. After his father"s death in 1614, his mother married his successor as bishop.
Peder Winstrup the younger studied at the universities of Rostock, Wittenberg, Leipzig, and Jena in Germany and graduated from the University of Copenhagen in 1633.
In 1635, he was appointed royal chaplain in the household of King Christian IV. He was awarded a doctorate in theology in 1636 and was made bishop of Lund in 1638. After Scania and the other provinces included in his diocese had been ceded to Sweden through the Treaty of Roskilde in 1658, Winstrup"s loyalty shifted to his new sovereign, Charles X Gustav, and he was ennobled under the name Himmelstierna, a name he never actually used. In 1658, he suggested that a new university should be founded in Lund, but received little response from the King.
When the Swedish authorities moved to found a university a few years later, at least some of the initiative lay with a subordinate priest in the diocese, Bernhardus Oelreich, and Winstrup turned to oppose the idea.
After the University of Lund was established in 1668, Oelreich was appointed the prokansler ("pro-chancellor"), despite the statutes giving this position to the Bishop. Winstrup was nevertheless appointed to this position in 1671.
Despite rumours accusing him for lack of loyalty to the Swedish crown, he remained bishop until his death in 1679. In June 2015 Winstrups grave was moved from the crypt of the Lund cathedral to its northern tower.
The body was taken away temporary for research.
lieutenant was in a well preserved condition. The body of a 6-month-old foetus was discovered in the Winstrup"s coffin, tucked in under the feet of the bishop, a common practice for burying foetuses and babies at the time.
