Montgomerie was the second son of Hugh Montgomerie, 7th Earl of Eglintoun and his second wife Lady Mary Leslie, daughter of John Leslie, 6th Earl of Rothes. He was educated at Glasgow in 1665. His uncle the 7th Earl had a sickly ward, Margaret Leslie daughter of Alexander Leslie, 2nd Earl of Leven, with whom he arranged a marriage for Montgomerie. Montgomerie married her under a financially advantageous contract dated 10 October 1673 which incurred a legal dispute when she died a year later in 1674. On 26 September 1679, he married as his second wife Elizabeth Primrose, widow of Sir James Primrose who died in 1702, and daughter of Sir Robert Sinclair, 1st Baronet of Longformacus, Berwickshire.
Montgomerie was returned as Shire Commissioner for Ayrshire in 1689. He was a member of the Scottish Privy Council from 1692 to 1708. In 1695 he was appointed a Director of the Company of Scotland.. Also in 1695, he was appointed Commissioner for auditing Treasury accounts. In 1696 he was appointed Governor of Dumbarton Castle and freeman of Dumbarton. He was Commissioner for Admiralty accounts in 1698 and was a Commissioner Justiciary for Highlands in 1701 and 1702. From1703 to 1708, he was Commissioner for the Scottish Treasury and from 1706 to 1707, a Commissioner for union with England.
In 1707, Montgomerie was one of the Scottish representatives to the first Parliament of Great Britain. He was returned as Member of Parliament for Ayrshire at the 1708 British general election. At the 1710 British general election, he withdrew in favour of his son John.
The date of Montgomerie’s death is unknown, but it preceded the sale of the Giffen estate in 1725. He had two sons, one of whom predeceased him, and two daughters.
- Foster, Joseph, ed. (1882), Members of Parliament, Scotland 1357-1882, Hazell, Watson and Viney, retrieved 21 June 2019
- "MONTGOMERIE, Hon. Francis (d. by 1729), of Giffen, Ayr". History of Parliament Online. Retrieved 26 May 2019.