Cromwell's religious policy included the maintenance of a national church, a policy acceptable to the army but much disliked by the Scots, who wanted the church to control the state, not the state the church. He improved the incomes of poor livings by revenues derived from episcopal estates and the fines of delinquents. An important feature of his church government was the appointment on the 20th of March 1654 of the "Triers," thirty-eight clerical and lay commissioners, who decided upon the qualifications of candidates for livings, and without whose recommendation none could be appointed; while an ordinance of August 1654 provided for the removal of the unfit, the latter class including besides immoral persons those holding "popish" or blasphemous opinions, those publicly using the English Prayer Book, and the disaffected to the government. Religious toleration was granted, but with the important exception that some harsh measures were enacted against Anglicans and Roman Catholics, to neither of whom was liberty of worship accorded. The acts imposing fines for recusancy, repealed in 1650, were later executed with great severity. In 1655 a proclamation was issued for administering the laws against the priests and Jesuits, and some executions were carried out. Complete toleration in fact was only extended to Protestant nonconformists, who composed the Cromwellian established church, and who now meted out to their antagonists the same treatment which they themselves were later to receive under the _Clarendon Code_ of Charles II.
Cromwell himself, however, remained throughout a staunch and constant upholder of religious toleration. "I had rather that Mahommedanism were permitted amongst us," he avowed, "than that one of God's children should be persecuted." Far in advance of his contemporaries on this question, whenever his personal action is disclosed it is invariably on the side of forbearance and of moderation. It is probable, from the absence of evidence to the contrary, that much of this severe legislation was never executed, and it was without doubt Cromwell's restraining hand which moderated the narrow persecuting spirit of the executive. In practice Anglican private worship appears to have been little interfered with; and although the recusant fines were rigorously exacted, the same seems to have been the case with the private celebration of the mass. Bordeaux, the French envoy in England, wrote that, in spite of the severe laws, the Romanists received better treatment under the Protectorate than under any other government. Cromwell's strong personal inclination towards toleration is clearly seen in his treatment of the Jews and Quakers. He was unable, owing to the opposition of the divines and of the merchants, to secure the full recognition of the right to reside in England of the former who had for some time lived in small numbers and traded unnoticed and untroubled in the country; but he obtained an opinion from two judges that there was no law which forbade their return, and he gave them a private assurance of his protection, with leave to celebrate their private worship and to possess a cemetery.