The crown as a decorative feature now became fashionable in honour of the return of the monarchy, and as an emblem of loyalty was much used as an ornament on furniture, especially on chairs. "Crown chairs" are still to be found in old Scots mansions, and in the Picture Gallery at Holyrood at least half the chairs are of this type and date from the Restoration period.

Little did the Leithers foresee they were welcoming to the throne the worst and meanest king who was ever to rule over them. If Cromwell had ruled them with rods, we shall see Charles, even in Leith, ruling the people with scorpions. He soon showed that no faith could be put in his plighted word. All he had promised while wandering in Covenanting company in search of a throne he now turned his back upon, and, by the most sternly repressive measures, sought to crush the Church of Scotland out of existence.

The struggle against the doctrine of the divine right of kings to do and rule as they pleased had all to be fought over again. The majority in Leith, as elsewhere in Scotland, chose the side of peace and immunity from persecution by conforming outwardly, at least, to the arbitrary decrees enforcing the Church policy of the Government. How untroubled and full of pleasure the lives of such conformists could be, and how gay a place Leith was, even during the torturings and violent deaths of the "killing time," we see from the account books of Sir John Foulis of Ravelston, the nephew of the Ladie Pilrig, who supplied the heather for the smeekers during the plague.

As we read in Sir John’s pages of his visits to the annual horse races on Leith Sands, of his golf matches on the Links, of his going to the play (enacted in all probability in the tenths court at the King’s Wark), of his dinners, and "sweeties" and oranges for the bairns at Mrs. Kendall’s fashionable tavern in the Kirkgate, and of the refreshments at Rob’s village inn at Restalrig, as they drove home in the great family coach, we would never suspect that men were being hunted and shot down among the hills and moors for no other crime than wishing to worship God as their fathers had done. There is not the faintest reflection of such things all through this record Sir John gives us of his daily life spent in Edinburgh and at Ravelston during this period. and yet even in Leith, while those who, like Sir John Foulis, conformed to the king’s policy in Church matters could and did follow a life of pleasure, men resisted the tyrannous measures of the king and were ready to risk all the penalties the "Bluidy Mackenzie" and his deputy, Sir William Purves of Abbeyhill, one of the elders in South Leith Church, might impose.

Among the four hundred ministers driven from their churches for holding that Christ and not King Charles was head of the Church were the minister of North Leith, and Mr. Hogg, the senior minister of South Leith, who escaped being imprisoned by fleeing to Holland, where he spent the rest of his days as minister of a Scots church in Rotterdam. The "outed" ministers began to preach the Gospel in private houses, where many gathered to hear them. The Conventicle Act declared such meetings illegal, and troops, quartered in the town, went through the streets and closes every Sunday in search of conventicles, and had their zeal in the work stimulated by the knowledge that a Government reward of £50 would be paid for every one they discovered.

Millers have always been noted, both in history and tradition, as stout and bold men. Thomas Stark, the miller at Leith Mills, by the waterside opposite Junction Road Station, was no exception to the rule. He was a stalwart supporter of the Covenant. His brother-in-law was the outed minister of Skirling. He went "afield," and held a conventicle, among other places, at Leith Mills in February 1675, when the whole company were arrested by a troop of soldiers under the command of Captain Ogilvie. Fines up to £100 were imposed on each attender, for in those days of corrupt courts of justice the Government depended on such sources for a large part of its revenue. Despite increased efforts on the part of the Privy Council to suppress them, the number of conventicles increased rather than diminished, and even in Leith and Edinburgh, the headquarters of the Government, it was found impossible to prevent the citizens from attending illegal religious meetings. Increasingly stringent measures were adopted to compel the people to attend the two parish churchs, but the conventicles continued nevertheless.

Although none of the great tragic events in this struggle between the king and his Scottish subjects took place in Leith, yet the town was more or less incidentally associated with several of them. The train-bands of Leith and Edinburgh were summoned by tuck of drum to muster on Leith Links and then join Monmouth’s forces against the Covenanters at Bothwell Bridge, when the incorporation of carters and the "poor brewers" of Leith had their horses and carts commandeered to form part of the baggage train. The prisoners captured in the battle, after a weary journey, during which none dared befriend them, were interned in the field then known as the Inner Greyfriar Yard, of which the long narrow southern extension of the famous churchyard, now known as the Covenanters’ Prison, formed only a small part.

After having been confined in their exposed prison for five months, two hundred and seven of the Covenanters were marched to Leith and put aboard a sailing vessel called the Crown, to be carried as slaves to the Plantations. There were sore hearts and streaming eyes among the Leithers as they saw the crowd of staunch but miserable Covenanters hustled through the street.

The captain of the Crown, "a profane, cruel wretch," used them most barbarously, but their sufferings were not to be for long. Their port was nearer than they anticipated, for, as some one has finely said, their sails were set to reach Jerusalem. On a dark and stormy night in December the ship, with her living cargo under closed hatches, was dashed to pieces among the Orkneys, and over two hundred of the wretched prisoners were drowned.

As the weary but undaunted prisoners from the Inner Greyfriar Yard passed down the Easter Road to the Shore of Leith, they might have noticed across the unenclosed fields, as it swung in chains at the Gallow Lee—Leith’s place of execution for all except pirates— part of the body of that once fearless fighter, David Hackston of Rathillet, who held the bridge of Bothwell for hours against the royalist troops, and who witnessed, but took no part in, the foul murder of Archbishop Sharp on Magus Moor in 1679. To the Gallow Lee many of the Covenanters were taken to their doom. It was a place of execution less public than the Grassmarket, where the farewell speeches of the martyrs deeply moved the crowds that came to see them done to death.

At the Gallow Lee the worst criminals were hung, to add reproach and ignominy to their death. Here, after Hackston’s remains had all been pecked away by the kites and crows, five Covenanters were hanged. Their bodies were buried beneath the gibbet, while their heads were spiked above the city gates. But good men and true, among whom was the youthful James Renwick, the last of the martyrs of the Covenant, came in the darkness and silence of night, dug up the headless bodies, and reverently buried them in the West Kirkyard (St. Cuthbert’s). They then boldly took down the heads from the city gates; but, daylight overtaking them before they could place these beside the bodies they buried them beneath two rose trees in a garden near the present Royal Infirmary, where, forty-six years later, they were accidentally discovered and reinterred in Greyfriars’ Churchyard beneath the Martyrs’ Monument.

From this time the persecution became fiercer than ever, and nowhere outside the Netherlands under Alva, could there have been a more complete system of tyranny than that set up for stamping out Presbyterianism. The minister of North Leith, a namesake of the great Reformer, was sent to the Bass Rock, then much used as a State prison for confining outed and disobedient ministers. His successor, like the two ministers of South Leith Church, was an Episcopalian, which would seem to show that the majority of the Sessions and parishioners of both churches, from choice or necessity, more probably the latter, had conformed to Episcopacy. Among the Session members of South Leith who favoured the policy of the king in Church affairs were Lord Balmerino, whose action in doing so was contrary to the traditions of his family, which had hitherto been staunchly Presbyterian. Sir Patrick Nisbet of Craigentinny; Sir William Purves of Abbeyhill, who, as assistant public prosecutor, had the odious duty of assisting "Bluidy Mackenzie" in persecuting the Covenanters; William Mylne, son of the King’s Master Mason; and Robert Moubray, whose great ancestor, Sir Philip Moubray, held Stirling Castle against Bruce, and whose last descendant in Leith, Mr. Robert Moubray, banker, still remembered by many in the town for his courtliness of manner, died in 1882.