When English Civil War broke out in England in 1642, Moore pledged his allegiance to the Roundhead Parliamentarians as did most of Liverpool's burgesses, who were largely of Puritan stock.
The nobles and gentry formed the bulk of the Cavaliers (who had control of both Liverpool Castle and tower), including the mayor, John Walker.
After the castle had been taken, John Moore assumed control of both it and the area that it encompassed, taking the title of Governor of Liverpool for himself.
Moore's victory was not to be long lived however, and Liverpool was routed from underneath him on 13 June 1644 when the Royalist Prince Rupert of the Rhine and his army of 10,000 forced an entry into the city around the area of Old Hall Street.
Moore was a supporter of Pride's Purge and, as well as helping to organise security arrangements at King Charles's trial.