Charles I's reign is largely marked by financial and constitutional struggles with the King, whose demands and trade restrictions alienated the City. On January 4th 1642, when the King tried to arrest five members of the House Commons for treason, they all fled to the City. He looked around Parliament in Westminster and commented, "The birds have flown". The following day, he personally demanded their surrender, at Guildhall, but to no avail; and he heard cries of 'Privileges of Parliament!" as he left. London naturally became an anti-royalist stronghold. The greatest threat to its dominant position came in November 1642 when the King's men, following the Battle of Edgehill, moved south to Brentford, nine miles from London. They were quickly put to flight by Lord Essex's men,, supported by a large group of Londoners, and were forced to fall back to Reading and Oxford. The next time Charles came to the capital would be in January 1649 for his trial in Westminster Hall and execution outside the Banqueting House at Whitehall Palace. His son, Henry VIII, was another great palatial builder. He expanded York House, the London residence of the Archbishop of York, to become the Palace of Whitehall, joining Westminster with Charing Cross. He also erected Bridewell Palace (the name derives from an ancient holy well), south of Fleet Street just west of the city, when the Royal apartments at Whitehall were wrecked by fire. New lodgings at Bridewell were needed to house the retinue of the Emperor Charles V when he visited London in 1522. Charles himself stayed with the Blackfriars next door. Henry also built St. James' Palace and the now lost Palace of Nonsuch. He confiscated Hampton Court from Cardinal Wolsey and added much of what we see there today. However, Henry's favourite residence was Greenwich Palace, where he had been born; and it thus became the scene of many important historical episodes during his reign. Like the Archbishops of York at Whitehall, the prelates from Canterbury had a London home across the river at Lambeth Palace. The complex was originally established in 1197 and a medieval chapel crypt survives where the hearings for Henry VIII and Anne Boleyn's divorce were heard. Most of the present building is Tudor including the Gatehouse and Great Hall. Its Lollards Tower was where the heretical followers of John Wycliff were imprisoned.

The Cromwellian period is notable for the return of a Jewish community to the City. Following their banishment by Edward I in 1292, there is little evidence of their having any presence at all in London. A small settlement of Jews from Spain and Portugal, fleeing the Inquisition, had reached London via Amsterdam during Charles I's reign. Cromwell was to employ them in his secret service and, eventually, he made Abraham Israel Carvajal, their official leader, the first English Jew. However, it was not until 1655, at a conference led by Rabbi Menasseh Bell Israel that it was finally agreed that English Law did not forbid the settlement of Jews. In 1657 a synagogue was openly built at Creechurch Lane in the City and a cemetery was allocated at Mile End. Restoration of the Monarchy The restoration of Charles II to the throne was to be followed by two great disasters: the first was the Great Plague of 1665, followed a year later by the Great Fire. Plague had been a constant threat in London since Medieval times. The outbreak of 1665 began in St. Giles-in-the-Fields and spread to devastate the over-crowded, impoverished areas of Stepney, Shoreditch, Clerkenwell, Cripplegate, St. Giles's and Westminster. Within the City itself, it was relatively controlled. In June, the King and his courtiers left London, not to return until February of the following year. A parliamentary session of only a few days was held at Oxford. The Duke of Albermarle was the only one of the King's ministers to remain in London. He was aided by magistrates, whom the King had ordered to stay, and he personally took responsibility for the areas beyond the city walls. The Lord Mayor, Sir John Lawrence, was responsible for the City. A fascinating insight into these appalling times can be gained from reading Daniel Defoe's 'Journal of the Plague Year,' as a description, though not strictly a history. Of nearly 100,000 deaths recorded in London in 1665, over 68,000 were the result of plague.

At the time of the great fire, plague was still present in London. Early in the morning of Sunday 2nd September 1666, a baker's shop in Pudding Lane, near London Bridge caught fire. The houses nearby were overcrowded and made of wood, and the fire quickly spread to the riverside where large quantities of highly combustible materials were kept. The early destruction of the water wheel at the bridge meant that the areas round about had no water supply with which to fight the fire. The fire spread rapidly into the heart of the City and was soon threatening the Royal Exchange, Lombard Street and Cornhill, a very wealthy area. The fire was driven deeper and deeper into the capital by a wind which blew constantly for the first three days. By the end of the second day, the riverside had been devastated and the fire had engulfed Cornhill, the Poultry and was threatening Cheapside. We have a very vivid account from the diarist, Samuel Pepys, who described the fire at night as a vast "bow of flame". As the means of directing water onto the flames were hugely inadequate, the only real way to fight the fire was to pull down the burning houses, before it could spread further. People used poles, axes, ladders - anything to try to prevent its spread