Queen Elizabeth was puzzling over the proper relationship between the crown and the church when Richard Hooker, a humble scholar, theologian, and clergyman, attempted to find a justification in reason for the establishment of the Church of England as an official part of the governing apparatus of the nation. His thinking was a turning point from the medieval notion that God ordered society, including the designation of its monarch and its natural laws, and the belief in a divine structure with a great chain of being, beginning with God and working down through the hierarchy of angels and saints to men, beasts, and vegetables, which structure fostered order in society. Hooker restated the concept of Aristotle that the purpose of society is to enable men to live well. He wrote that although the monarch was head of state and head of religion, the highest authority in civil affairs was Parliament, and in religion, the Convocation. The monarch had to maintain divine law, but could not make it. From this later came the idea that the state derives its authority from the will of the people and the consent of the governed.
Protestant women had more freedom in marriage and were allowed to participate in more church activities compared to Catholic women, but they were not generally allowed to become pastors. Due to sensitivities on the part of both Catholics and Protestants about a female being the head of the church, Elizabeth was given the title of "Supreme Governor" of the church instead of "Supreme Head". Elizabeth was not doctrinaire in religious matters, but pragmatic. She always looked for ways to accommodate all views on what religious aspects to adopt or decline. Images, relics, pilgrimages, and rosaries were discouraged. But the Catholic practice of kneeling at prayer, and bowing and doffing caps at the name of Jesus were retained. Also retained was the place of the altar or communion table at the east end of churches, special communion wafers instead of common bread, and elaborate clergy vestments. The communion prayer contained words expressing both the Catholic view that the wafer and wine contained the real presence of the body and blood of Christ, and the Protestant view that they were commemorative only. Communion was celebrated only at Easter and other great festivals. Church services included a sermon and were in accordance with a reformed prayer book and in English, as was the Bible. Care was even taken not to use words that would offend the Scots, Lutherans, Calvinists, or Huguenots. People could hold what religious beliefs they would, even atheism, as long as they maintained an outward conformity. Attendance at state church services on Sunday mornings and evenings and Holydays was enforced by a fine of 12d. imposed by the church wardens. Babies were to be baptized before they were one month old or the parents would be punished.
The new religion had to be protected. Members of the House of Commons, lawyers, schoolmasters were to take the oath of supremacy or be imprisoned and make a forfeiture; a second refusal brought death. When numerous Anabaptists came from the continent to live in the port towns, the Queen issued a proclamation ordering them to leave the realm because their pernicious opinions could corrupt the church. The new church still accepted the theory of the devil causing storms, but opposed ringing the holy church bells to attempt to drive him away. The sins of people were also thought to cause storms, and also plagues.
In 1562, the Church of England wrote down its Christian Protestant beliefs in thirty-nine Articles of Religion, which specifically excluded certain Catholic beliefs. They were incorporated into statute in 1571 establishing them as the tenets of the official religion of England. The first eighteen endorsed the ideas of one God, Christ as the son of God who was sacrificed for all the sins of men, the resurrection of Christ from the dead and ascension into heaven, the Holy Ghost proceeding from the father and the son, the books of the Bible, the original sin of Adam and his offspring, justification of man by faith in Christ rather than by good works, goods works as the inspired fruit and proof of faith in Christ, Christ in the flesh as like man except for the absence of sin, the chance for sinners who have been Baptised to be forgiven if they truly repent and amend their lives, the predestination of some to be brought by Christ to eternal salvation and their minds to be drawn up to high and heavenly things, and salvation only by the name of Christ and not by a sect. Other tenets described the proper functions of the church, distinguishing them from Roman Catholic practice. Specifically, the church was not to expound one place of scripture so that it was inconsistent with another place of scripture. Because man can err, the church was not to ordain or enforce anything to be believed for necessity of salvation. Explicitly renounced were the Romish doctrine concerning purgatory, pardons, worshipping, adoration of images or relics, invocation of saints, and the use in church of any language, such as Latin, not understood by the people. Only the sacraments of Baptism and the Lord's Supper were recognized. The Lord's Supper was to be a sign of the love that Christians ought to have among themselves and a sacrament of redemption by Christ's death. The wine in the cup of blessing as well as the bread of the Lord's Supper was to be taken by lay- people and to be a partaking of Christ; there was no Romish mass. Excommunication was limited to those who openly denounced the church. Anyone openly breaking the traditions or ceremonies of the church which were approved by common authority were to be rebuked. Elizabeth told the bishops that she wished certain homilies to be read in church, which encouraged good works such as fasting, prayer, alms-giving, Christian behavior, repentance, and which discouraged idolatry, gluttony, drunkenness, excess of apparel, idleness, rebellion, and wife-beating, however provoked. She considered homilies more instructive and learned than ministers' sermons, which were often influenced by various gentlemen and were inconsistent with each other. Consecration of bishops and ministers was regulated. They were allowed to marry. The standard prayer was designated thus: "Our Father who art in heaven, hallowed be Thy name. Thy kingdom come. Thy will be done, on earth as it is in heaven. Give us this day our daily bread, and forgive us our offenses as we forgive those who have offended against us. And lead us not into temptation, but deliver us from evil. For Thine is the kingdom, the power, and the glory forever and ever, amen."
There was difficulty persuading educated and moral men to be church ministers, even though Elizabeth expressed to the bishops her preference for ministers who were honest and wise instead of learned in religious matters. The Bible was read at home and familiar to everyone. This led to the growth of the Puritan movement. The Puritans believed in the right of the individual Christian to interpret the Scriptures for himself by spiritual illumination. They opposed the mystical interpretation of the Communion service. The Puritans complained that the church exerted insufficient control over the morals of the congregation. Their ideas of morality were very strict and even plays were thought to be immoral. The Independent Puritans were those Protestants who had fled from Mary's Catholic reign to the continent, where they were persuaded to the ideas of John Calvin of Geneva. He stressed the old idea of predestination in the salvation of souls, which had in the past been accepted by nearly all English Christian leaders, thinkers, and teachers, but not stressed. The act of conversion was a common experience among the early Puritans. The concomitant hatred of past sins and love of God which was felt in thankfulness for mercy were proof of selection for salvation. The good works that followed were merely an obligation showing that one's faith was real, but not a way to salvation.
The puritans also accepted Calvin's idea of independent church government. They therefore thought that ministers and lay elders of each parish should regulate religious affairs and that the bishops, who were "petty popes", should be reduced to an equality with the rest of the clergy, since they did not rule by divine right. The office of archbishop should be eliminated and the head of state should not necessarily be governor of the church. These ideas were widely disseminated in books and pamphlets. The puritans disrupted the established church's Sunday services, tearing the surplice off the minister's back and the wafers and wine from the altar rail. The puritans arranged "lectures" on Sunday afternoons and on weekdays. These were given gratuitously or funded by boroughs. They were strict about not working on the Sabbath, which day they gave to spiritual exercises, meditations, and works of mercy. The only work allowed was preparing meals for themselves, caring for their animals, and milking the cows. They enforced a strict moral discipline on themselves. The puritans formed a party in the House of Commons.
The puritan movement included William Brewster, an assistant to a court official who was disciplined for delivering, upon pressure from the council, the Queen's signed execution order for Mary of Scotland after the Queen had told him to hold it until she directed otherwise. After exhausting every other alternative, the Queen had reluctantly agreed with her Privy Council on the execution in 1572 of Mary, Queen of Scots, who had been involved in a plot to assassinate her and claim the throne of England. Elizabeth's Council had persuaded her that it was impossible for her to live in safety otherwise.
The debased coinage was replaced by a recoinage of newly minted coins with a true silver weight.
Goldsmiths, who also worked silver, often acted as guardians of clients' wealth. They began to borrow at interest at one rate in order to lend out to traders at a higher rate. This began banking.
Patents were begun to encourage the new merchant lords to develop local manufactures or to expand import and export trade. Patents were for a new manufacture or an improved older one and determined the wages of its trades. There was chartering of merchant companies and granting of exclusive rights to new industries as monopolies. Some monopolies or licenses were patents or copyrights of inventors. Others established trading companies for trade to certain foreign lands and supporting consular services. People holding monopolies were accountable to the government. There were monopolies on certain smoked fish, fish oil, seal oil, oil of blubber, vinegar, salt, currants, aniseed, juniper berry liquor, bottles, glasses, brushes, pots, bags, cloth, starch, steel, tin, iron, cards, horn, ox shinbones, ashes, leather pieces, earth coal, calamite stone, powder, saltpeter, and lead manufacturing by-products.