Pont's legal skill allowed him to be made Provost of Trinity College, and through the influence of Morton, but with the consent of the Assembly, he accepted a seat in the Court of Session in 1572.

[13] As a commissioner representing St. Andrews, Robert Pont was present at the very first meeting of the General Assembly of the Church of Scotland, held in Edinburgh on 20 December 1560.

[14] After visiting, he confessed his inability, on account of his ignorance of Gaelic, to carry out his duties; but on the understanding that he was not to be in charge of Gaelic-speaking churches, he accepted a renewal.

By the assembly which met in December 1567 he was commissioned to execute sentence of excommunication against Adam Bothwell, bishop of Orkney, for performing the marriage ceremony between the Earl of Bothwell and Mary Queen of Scots; by that in July 1568 he was appointed one of a committee to revise the Treatise of Excommunication originally penned by John Knox; and by that in 1569 he was named one of a committee to proceed against the Earl of Huntly for his adherence to popery.

He attended the convention which met at Leith in January 1571–2, and following this meeting he was permitted to accept the office of Senator of the College of Justice (also later known as a Lord of Session), given to him by the regent John Erskine, Earl of Mar on account of his knowledge of the laws.

[13] Pont was one of those who, after the fall of the regent James Douglas, 4th Earl of Morton in 1578, accompanied the English ambassador to Stirling to arrange an agreement between the faction of Morton and the faction of Atholl and Argyll; and he was also one of those who, nominally at the request of the king James VI, convened in Stirling Castle, on 22 December 1578, for the preparation of articles of a Book of Policy, later known as the Second Book of Discipline.

He took a prominent part in the proceedings in 1582 against Robert Montgomery in regard to his appointment to the bishopric of Glasgow; and at a meeting of the privy council on 12 April he protested in the name of the presbyteries of Edinburgh, Stirling, and Dalkeith that the cause was within the jurisdiction of the kirk.

[13] In 1583 Pont was appointed one of a commission for collecting the acts of the assembly; and the same year was directed, along with David Lindsay and John Davidson, to admonish the king to beware of innovations in religion.

When the acts of parliament regarding the jurisdiction of the kirk were proclaimed at the market cross of Edinburgh on 25 May 1584, Pont, along with Walter Balcanqual, made a public protest.

On 7 November he was summoned by the privy council to appear before it on 7 December, and give reasons for not subscribing the "obligation of ecclesiastical conformity"; shortly before this he had returned to Scotland, and had been put in ward, but not long afterwards he received his liberty.

The same year he was appointed by the assembly as one of a committee for collecting the various acts of parliament against papists, with a view to their confirmation on the king's coming of age; and in 1588 he was appointed one of a committee to confer with six of the king's council regarding the best methods of suppressing Catholicism and extending the influence of the kirk; and also one of a commission to visit the northern parts, from the River Dee to the diocese of Caithness inclusive, with a view to the institution of proceedings against Catholics, the planting of kirks with qualified ministers, and the deposition of all ministers who were unqualified, whether in life or doctrine.

[13] When the Act of Abolition granting pardon to the Earls of Huntly, Angus, Erroll, and other Catholics on certain conditions was on 26 November 1593 communicated by the king to the ministers of Edinburgh, Pont proposed that it should be disannulled rather than revised.

At the General Assembly which met in March 1597–8 he was one of the main supporters of the proposal of the king that the ministry, as the third estate of the realm, should have its own vote in parliament.

He had had a tombstone prepared for himself, with epitaphs written by himself, but this was removed and another set up by his widow, Mary Smyth, which remained by a privy council decision in June 1607.

Robert Wodrow stated that Pont had a "discovery" (correct prediction) of the date of Queen Elizabeth's death, which he told to James VI.