He was incorporated at Oxford on 11 July 1671, as one of the first four Scots who benefited by Bishop John Warner's exhibitions intended for Balliol College.
In 1686 he was forbidden by the Inquisition to continue his functions, although he pleaded a traditional privilege, founded on the treaty between England and Portugal.
The English merchants wrote immediately to Henry Compton, bishop of London, to assert their rights; but before their letter reached its destination Geddes was suspended by the ecclesiastical commissioners appointed by James II.
Matters had to await the arrival of Charles Scarborough, the English envoy, and Geddes returned in May 1688 to England,.
Gilbert Burnet as bishop of Salisbury collated Geddes to the chancellorship of his cathedral on 12 June 1691.