Following the Restoration of King Charles II, he declined to accept the authority of the newly imposed bishops in the Kirk.

[3] On 3 September 1672 he declined indulgence at Kilwinning, disobeyed a citation of the Privy Council, and fled to London, where his Scottish speech somewhat marred his usefulness.

He speaks of an ‘extraordinary impression’ made upon him as a boy by a voice which he heard when he had climbed up into his father's pulpit at night; but he dates the beginning of his religious life from a communion day at Greyfriars Church, Edinburgh, at the opening of 1648.

At the battle of Dunbar (3 September 1650) he was probably in the ranks of the Scottish army, for he speaks of his ‘signal preservation.’ After license he received a call to Cambuslang, Lanarkshire, and was ordained there in 1653.

[6] Following the defeat and execution of King Charles I, and the conquest of Scotland, by the New Model Army of Oliver Cromwell, Fleming was called to be Minister of Cambuslang, when only 24.

On 30 December 1677 he was admitted colleague [in succession to Robert MacWard] to John Hog [or Hoog], minister of the Scots Kirk, Rotterdam.

Brought before the privy council in June 1679, he agreed to give bail, but declined to promise a passive obedience.

The Privy Council allowed him bail, June 1679, but refusing to conform to all its demands, he was sent back to confinement.

He did not formally demit the charge of Cambuslang till March 1688, on the death of David Cunningham, who had been appointed in his place.

[5] Fleming left a diary, which was not published; his rather confused list of thirty-eight memorable occurrences of his life, entitled A Short Index, &c., is printed at the end of Memoirs by Daniel Burgess, prefixed to the 1726 edition of the Fulfilling and in Howie's Scots Worthies.

[11] Wodrow characterises Fleming as a "devout and pious man, most spiritual in his carriage and writings, much engaged in secret prayer and meditations, very affectionate to his servants and people, full of love, and of a peaceable temper.