It's odd to think that despite the underlying friction between the English troops and Leithers due to the people of Leith supporting Charles II. Things did settle down and gradually a air of normality descended onto Leith and new industries appeared like glass making in North Leith. The first newspaper in Scotland appeared under the name "Mercuicus Politcus" which was printed in the Citadel at North Leith and from this we learn that many soldiers settled down and married in Leith. Not only was glass made but the Linen industry was developed. For the first time the position of Leith in respect to Edinburgh was being recognised. In fact according to General Monck Commander of the Parliament forces in Scotland observed that he had never seen a town so domineered by another(meaning Leith being domineered by Edinburgh). However despite being under military rule nothing was done about this and Edinburgh kept control over Leith. In fact Leith had to wait a further 283 years before Leith became independent of Edinburgh and several hundred years of injustice was ended (only to be reimposed in 1920 when Leith was, against the wishes of Leithers, amalgamated into Edinburgh and deeply resented ever since). In the Coronation procession of Charles II Monck rode behind the King as Master of the horse. He is the only soldier to have been both a General and a Admiral in a long a distinguished military career.

Scotland as a whole was in a bad way in 1651. It had been defeated at Dunbar and Worcester and despite continuing fighting in the highlands. Scotland which in many ways resisted many potential conquerors like the Romans, Norman's and Saxons had at long been conquered. However Cromwell didn't look on Scotland as a enemy only misguided and only had to be shown the right way. However the truth of the matter was the Covenanting movement was in disarray and as a national force it was finished. That is why when the "Killing times" came it didn't really affect Leith. However it did involve Leith up to a point.

When Charles II came to the throne at the Restoration in 1660 he didn't forget the price of his crown was the signing of the National Covenant which he didn't want to do and he had to say sorry and show repentance for his sins and his whole family for which Charles never forgave the Church of Scotland or its Presbyterian Government. So once in power he set out to crush the ideals of the National Covenant once and for all. The first to suffer was the Marquis of Argyll (who had crowned Charles II and was one of the most powerful Lords of the Clan Campbell), in December 1661 Argyll was conveyed to Leith by the warship Eagle and met by the Water Bailie and his deputy on the Shore and taken to Edinburgh where he was later executed. He had been betrayed by Monck.

The Episcopalian Church was imposed on Scotland and over 400 ministers who refused to conform were forced to leave their Churches and had to preach in the open fields and private houses, the so called "Conventicles" which by the Conventicle Act was made illegal. People like Sir John Foulis agreed with the Kings Church Policy and the actions of "Bloody Mackenzie" who's deputy in persecuting the covenanters was Sir William Purves of Abbyhill who was one of the Elders at South Leith Church created fear in Scotland. However in the eyes of the Covenanters Christ was head of the Church not the King and refused despite all the hardships to give up what they knew to be true.