Forging a broad base of support for the new republican regime proved to be a difficult task for Cromwell, and the Rump Parliament was a chronic disappointment in this regard. A powerful group of nobles known as the Independents refused to be publicly associated with the idea of a republic–among them the important Parliamentarians Wharton, Saye, and Sele. Like Cromwell, Saye, Wharton, and Sele thought that England needed some form of monarchic power to remain strong. Parliament took an important first step toward unified government on February twenty-four, 1652, when it passed an Act of General Pardon and Oblivion that unilaterally forgave all of Charles I's supporters and removed them from the threat of prosecution.

Cromwell viewed such conciliatory policy as necessary, but in some ways the Rump Parliament proved too conservative for Cromwell's tastes. He was particularly impatient with the Rump Parliament's failure allow religious freedom for all Protestant sects. Quite suddenly, Cromwell put a violent end to the Rump Parliament on April twenty, 1653. In a fiery speech he gave that day, Cromwell insulted many of the MPs and accused them of corruption. He then ordered armed men to clear the members of Parliament out of the chamber. On April thirty, Cromwell announced that the state would now be administered through a ten-man Council of State.

This was the first major step toward Cromwell's dictatorship, although in the following weeks he specifically denied that that he wished to establish any sort of autocracy. Instead, Cromwell insisted that Parliament had not been dissolved by his authority, but merely suspended until it could behave in a manner more appropriate for the new republic. In its place, Cromwell designed a new parliament, made up of 144 men of "approved fidelity and honesty." Cromwell monitored the selection of these men very closely, making sure that they shared his political and religious ideals. For the most part, the members of this new parliament were from a lower social status than was usual, lesser gentry like Cromwell himself. The parliament received the nickname "Barebones Parliament", after the surname of one of its more colorful members, a London leather merchant and Puritan named Praise-God Barebones. The Barebones Parliament primarily discussed practical ways in which to rationalize the taxation system. It also debated the elimination of tithes, the portion of income some English subjects were required to give to the church. Parliament legalized civil marriages and debated a proposed unification of England and Scotland.

Cromwell soon grew impatient with the Barebones Parliament. This time, however, he was angered by their radicalism rather than by their conservatism. Cromwell disagreed with Parliament's enthusiasm for an ongoing war, fought mainly for trade interests, with the Dutch, and he disliked the hostility many members showed toward the landed nobility and greater gentry. Cromwell was further disgusted by the Barebones Parliament's intolerance toward the conservative Presbyterians and by their opinions on the structure and power of the Army. The Barebones Parliament was not a nuisance to Cromwell for long, however. In a surprise maneuver in December of 1653, eighty of the Barebones Parliament's members abruptly resigned their seats, effectively turning power back over to Cromwell. It remains unclear whether or not Cromwell was actually responsible for the resignations. At any rate, Cromwell and his council of officers met to discuss new ways to run the regime. Shortly after gathering, the council passed a resolution creating a twenty-one-member Council of State, and Cromwell was proclaimed England's Lord Protector.

The ceremony for Cromwell's installment as Lord Protector took place with little pomp. Nonetheless, Cromwell soon came to wield king-like power and receive almost royal treatment. In fact, in April 1654 Cromwell moved with his wife Elizabeth and his elderly mother to Whitehall Palace, where Charles I had once held court. Cromwell was addressed by English subjects and foreigners alike as "Your Highness", and by 1656, his Council of State was known by the name Privy Council, which was the name of the former advisory council of the English kings.