In 1615 he became rector of Allhallows, Lombard Street, and held the benefice with his other preferments till his elevation to the episcopate.
In 1629 he seems to have been chaplain to the English ambassador in Paris; he forwarded to William Laud a petition from a John Fincham, in France on the king's service and imprisoned in the Bastille.
He was consecrated bishop of Peterborough at Lambeth by Archbishop Laud, assisted by William Juxon, on 18 May 1634, and was enthroned by proxy on 28 May.
In his diocese, as elsewhere, the order for placing the communion table altarwise at the east end of the chancel, and fencing it in with rails, produced discontent among the clergy, and Dee received frequent instructions from the high court of commission to proceed against those who refused to obey.
By his will, dated 28 May 1638, he donated to the repair of his cathedral, and to St. John's College the impropriate rectory of Pagham for the foundation of two scholars and two fellows to be chosen from Peterborough grammar school.