There were two sessions the first from 17 September 1656 until 26 June 1657 and a second from 20 January until 4 February 1658. The Second Protectorate Parliament was summoned reluctantly by the Lord Protector Oliver Cromwell on the advice of the Major-Generals who were running the country as regions under military governors. The Major-Generals thought that a compliant parliament would be the best way to raise money to pay for the Army occupation, and the Navy both of which were involved in the Anglo-Spanish War (1654–1660).
The elections were held under the new written constitution called Instrument of Government. It included returning up to thirty members from Scotland and up to another thirty from Ireland. Royalists and Catholics were prevented from standing or voting under Articles XIV and XV. After the election the Council of State stopped one hundred elected members from taking their seats by declaring that they were not "of known integrity, fearing God" (Article VII). A further fifty withdrew in protest which left about two hundred and fifty to take their seats for the first session.
The first session opened in December 1656. The Protectorate government did not have much pressing legislation to present so the House occupied its time with private members bills. However over the next few months three issues would dominate the session. The first was the Militia Bill, the second was the Naylor case and the third was constitutional reform (the Humble Petition and Advice), which was influenced by the failure of the Militia Bill to pass and the Naylor case was to show that the members of Parliament were less religiously tolerant than was constitutionally allowed in Instrument of Government.
The House voted down Major-General John Desborough's "Militia Bill" on 29 January 1657 by one hundred and twenty four votes to eighty eight. This bill would have perpetuated the Decimation Tax that funded the mounted militia, which was collected by Cromwell's Major-Generals; the failure of the bill caused the so-called rule of the Major-Generals in the counties to end.
With the rejection of the Decimation Tax, it was clear that government through the Major-Generals could not continue. In February 1657 Cromwell was offered the crown and a new constitution called the Humble Petition and Advice.