In August 1648 the parliamentary army defeated the Scots and once again Charles I was taken prisoner. Now that Parliament was in control of England its members began to argue amongst themselves. Most Members of Parliament were Presbyterians. These men were willing to share power with the king. Presbyterians also had strong feelings on religion. They disapproved of other puritan groups such as the Anabaptists, Quakers and Congregationalists and wanted them suppressed.

The other major group were called the Independents. They tended to be followers of the religious groups that the Presbyterians wanted to suppress. The Independents argued for a policy of religious toleration. Some Independents also wanted to bring an end to the monarchy.

The Independents had a strong following in the New Model Army and had the support of Oliver Cromwell. Afraid of their power, Presbyterianmembers of the House of Commons tried to disband the army. The soldiers were furious, especially as Parliament made no effort to pay them the wages that were due to them. The army decided to take action. The Presbyterians were expelled from Parliament. With the Independents now in control, it was decided to put Charles II on trial as a traitor. In 1649 Charles was found guilty and executed outside his Whitehall Palace.

The Independents now passed a series of new laws. The monarchy, the House of Lords and the Anglican church were abolished. Lands owned by the royal family and the church were sold and the money was used to pay the parliamentary soldiers. The Independents also kept their promise regarding religious toleration. People were no longer fined for not attending their local church. However, everyone was still expected to attend some form of religious worship on Sundays.