As Lord Protector, Oliver Cromwell called two separate parliaments to session, but his relationship with Parliament was often rocky. Cromwell's relationship with the first Parliament he called was particularly bad, and ended in 1655 with Cromwell forcibly disbanding the legislative body. Cromwell was frustrated by Parliament's need for lengthy deliberation, and by the fact that they frequently failed to see eye-to-eye on what reforms were needed. For their part, many members of Parliament resented Cromwell's enormous power, and spent a number of sessions debating the proper role of Parliament in the English government and deliberating the creation of an official constitution. Ironically, much of this debate was due to Cromwell's policy of redistributing Parliamentary seats to better reflect the country's local interests. This redistribution had brought an influx of landed country gentlemen–Cromwell's own social class–into Parliament, and this group proved to be among the most opposed to Cromwell.

Although Cromwell had great personal influence on a number of members of Parliament, he was unable to muster the support he needed and became somewhat distant even from his political allies. Cromwell further alienated his former cronies when he forced the members of Parliament to sign a "Recognition" of their belief in his system of government. To Cromwell's chagrin, a hundred members chose to resign rather than sign the document. By the end of 1654, Cromwell felt politically isolated, and this feeling intensified when one of his Council members, Ashley Anthony Cooper, defected. Like Cooper, most of Cromwell's opponents were conservatives angered by Cromwell's refusal to turn the Protectorate into a hereditary position.

Cromwell's political isolation coincided with a bad riding accident that left him incapacitated for three weeks. In October of 1654, Cromwell fell from his horse, causing a pistol in his pocket to go off and seriously injure his leg. Additionally, Cromwell's elderly mother died in November of that same year.

Frustrated and angry, Cromwell dissolved the House of Commons on January twenty- two, 1655. In a speech he delivered that day, Cromwell reprimanded the members of Parliament for deliberating on constitutional questions rather than enacting his plans for a Reformation. "If it be my liberty," Cromwell lectured them, "To walk abroad in the fields yet it is not my wisdom to do so when my house is on fire."

After disbanding Parliament and crushing Penruddock's Rebellion in March of 1655, Cromwell felt more than ever that the Reformation was being threatened from all directions. Consequently, Cromwell tried to suppress the opposition by ordering a severe crackdown on public debate and imposing a policy of strict state control over the press. A three-man censorship committee was appointed, and within a month of its establishment, all publications other than the two state-run newspapers were suppressed. In the summer of 1655, Cromwell appointed eleven major-generals to supervise the government of the English provinces. Although this action seems aggressive, it should be noted the generals were appointed partly in order to help the provinces build local militias so that the standing army could be reduced in size. Cromwell also charged his appointees with enforcing the ideals and standards of Puritanism and make sure that vices such as drinking and dressing immodestly did not persevere in the countryside.

For most of 1655 and the beginning of 1656, Cromwell governed without a parliament. This period also marked one of Cromwell's great gestures of religious tolerance, when he appointed a commission to consider the petition of Menasseh ben Israel, a Jewish leader who asked that the Jews be permitted to live and worship in freedom in England. Although ben Israel's petition was not formally honored, Cromwell sanctioned the unofficial return of Jewish people to England, reversing a policy that dated back to the thirteenth century. Cromwell's decision was, however, motivated in part by a desire to convert the Jews, which he believed would bring England one step closer to holiness.