On 9th January 1449 the Bishop of Chichester was murdered near the Domus Dei, by seamen, for failing to pay the wages due to them. For this crime, the town was placed under the Greater Excommunication, and as matters went badly with the inhabitants in the years that followed they attributed their misfortunes to this cause. The excommunication was lifted in 1508.

In 1494, by order from King Henry VII, the Square Tower at the end of the High Street was built and so too was the adjacent Platform. After 1540 it was used as a magazine, and it was due to Colonel Goring`s threat to fire the powder inside that he obtained generous terms of surrender for himself and his followers when the Forces of Parliament besieged the town in 1642.

In June 1495, the King gave orders for the construction of a dry dock at Portsmouth, the first known to have been built in this country. The Sovereign was the first ship to enter the dock on 25th May 1496. The docking process took 140 men in addition to the Mariners.