The Charter of 1106 was stolen along with the records of the Customs and Usages of the town in the 13th Century, while the Charter of 1313 was not only stolen it was also offered for sale in the streets of Portsmouth in 1546. It has been recovered but the Corporation had to pay £47 for it, as the last holder had purchased it at an auction sale.

In 1561 Queen Elizabeth paid her first visit to Portsmouth and happily resolved to use her great power and ingenuity for its development. Queen Elizabeth at great expense fortified Portsmouth. The expense of erecting these fortifications and others by Elizabeth were paid for from the profits of the first State Lottery. The scheme consisted of 400,000 tickets of ten shillings each, the first prize being £5,000 made up of £3,000 in cash with £700 worth of plate and the rest in tapestries and linens. Twenty five prizes were of the value of £100 or more.

The former residential portion of the Domus Dei which had been used as an armoury since the Dissolution of the Monasteries in 1540, was in 1658 converted into a residence for the Governor, and as such it continued for 300 years. Many famous people were entertained there, and it was in the great hall of the building that the wedding of Catherine of Braganza and king Charles II was celebrated. Its last official use was when the Allied Sovereigns were entertained there in 1814.