Bellenden was the son of Sir John Bellenden of Auchnoul, Lord Justice Clerk, and Barbara Kennedy, daughter of Sir Hugh Kennedy of Girvanmains by his spouse Janet Stewart, daughter to John Stewart, 2nd Earl of Atholl.
He was promoted to the bishopric of Dunblane, receiving a Crown provision on 24 September 1615 and was consecrated by April of the following year.
Balfour Paul states that he was also appointed, c. 1633, Dean of the Chapel Royal at Stirling Castle, and also held, as a personal right, Kilconquhar, succeeding to it upon the death of his nephew James, which was ratified in parliament in 1629.
He was appointed to Charles I's privy council in March 1626 and attended far more sessions than any other Scottish bishop.
One contemporary recorded how his lodgings in Old Aberdeen were plundered by Covenanters in 1640 and that Bellenden 'escaping himselfe, he lived quietlie in ane husbandman's house' (possibly in Aboyne) before moving south to England.