In September, 1650, Cromwell defeated the Scottish Presbyterian or Royalist army, under General Leslie, at Dunbar. He soon after entered Edinburgh, and from thence went "peaceably with his whole army and cannon, by way of Kilsyth to Glasgow." While on his journey he was informed by a messenger from the republicans of the city, that it was intended by the Presbyterians to destroy his army as it entered the city by the Stablegreen port. A vault beneath the archbishop’s castle had been filled with gunpowder, so the story went, which it was intended to fire as the troops marched past. Some have regarded this as merely a practical joke, but Cromwell took it seriously and changed his route, by turning to the right. Entering the city by the Coweaddens and the Cowloan, now known as Queen Street, he made his way to the Saltmarket, where he took up his lodging in what was known as Silvercraigs House, situated at the northern corner of Steel Street and nearly opposite the Bridgegate.

Arriving in Glasgow on Friday afternoon, 24th October, 1650, he found that the magistrates, ministers, and leading inhabitants had fled; but this was unnecessary, as that morning Cromwell, "at a rendezvous, gave a special charge to all the regiments of the army to carry themselves civilly and do no wrong to any." It is also stated "that the town of Glasgow, though not so big nor so rich, yet to all seems a much sweeter and more delightful place than Edinburgh, and would make a gallant headquarters were the Carlisle forces come up."

On his arrival, Cromwell sent for Patrick Gillespie, minister of the Outer High Kirk. This divine was well entertained, and when leaving, his august host treated him to such a long and unctuous prayer that Gillespie was constrained next day to make known his impression, or conviction, that Cromwell was one of the elect.

On the Sunday following his entry into the city, Cromwell and his officers made a procession to the Cathedral to hear sermon. Zachary Boyd, minister of the Barony parish, was the preacher for the day, and as he was a man of great boldness, he did not hesitate to rail on them all to their very faces.

It has been found from a manuscript note upon the preacher’s own Bible, that "the fantastic old gentleman," as Carlyle styles him, chose for his text Daniel, chapter viii., drawing a parallel between the rough he-goat and the Protector. So enraged was Thurlow, the secretary to Cromwell, that he asked leave—

"To pistol the old scoundrel."

"Tuts," replied the Protector, "you are a greater fool than himself. We’ll pay him back in his own coin

He aceordingly invited his reverend foe to dinner, which was of the scantiest and plainest kind, held pious converse with him during the evening, and wound up with a three hours’ prayer, which lasted till 8 o’clock in the morning. Boyd left rather pleased than otherwise, although he does not seem to have become a partisan of the Protector, as Gillespie appears to have been.

Cromwell also visited the University, and being informed by Gillespie that King Charles I. had promised to give £200 for the Library and Fabric of the College of Glasgow, but had never paid it, he, after some delay, not only caused the £200 to be paid, but also, on his own part, made a grant of £500 for the same purpose. Cromwell and his army left Glasgow next day, and the same authority previously quoted states: "I do not hear of the least injury that the soldiers offered to any during our abode there. And they (the citizens) say, that if ever we come that way again, they will persuade their friends to abide at home."

Baillie, who succeeded Gillespie as Principal of the University, and who was evidently not very favourably disposed towards his predecessor, although he was one of those who fled from the city before the Protector’s visit, has the justice to state:-