It was under Henry VIII’s young son and successor, Edward VI, that the Church of England became more thoroughly Protestant. Edward had been raised a Protestant, and his devotion to the new faith became more apparent as he grew toward adulthood. Radical Protestants who had sought shelter abroad during the reign of Henry VIII flocked back to England, unauthorized preaching occurred, as did the destruction of church ornaments and paintings which were seen by some Protestants as idolatrous and blasphemous.

Such radicalism was not what the government, under the leadership of Edward Seymour, Duke of Somerset and Lord Protector, had intended. Such behavior was seen as threatening to the sociopolitical order. Such active Protestants were, however, confined to a minority. In all likelihood, most people were still basically Catholic. Catholicism had been the religion of the country for so long that converting people to the new faith could not take place quickly. In an age that had no televisions or radios, people relied on the word of mouth to hear the latest news, and to be given instructions from the government. The further away people lived from the capital city of London, the harder it was for the government to control them. Sometimes it took up to a week for important news from London to reach the northern parts of England or some parts of Wales. The government had deputies in the local community, but it took time for news and instructions to reach even them, and time for these deputies to tell the local people what they were instructed to. The Church was the main centre of communication, and the local people would flock there to hear what was happening in the rest of the country and the rest of the world. Although the government could give instructions for the Protestant faith to be celebrated throughout the land, the implementation of this depended on the deputies in the local community, and the quality of the religious leaders. Some of the ministers were very poorly educated and did not really understand the Protestant faith themselves, and so could not teach it to their congregations.

At first, the Church under Edward differed little from that of his father. Stripping the church of its Catholic relics was continued and encouraged, as was the reading of the Bible in England and Cranmer's Homilies, Protestant sermons. But slowly the Church began to move in a much more Protestant direction.

In 1547 there was the Chantries Act, which meant that the chantries and their associated institutions were dissolved. This was initially a great loss to the country, not so much for the chantries themselves, but because of the closure of the colleges and hospitals associated with them. This however gave the impetus for schools to be secular institutions, which in the long run improved the quality of education in the country substantially. Hospitals were also increasingly secularized and in 1549 an act was passed allowing priests to marry. The main development in these years was, however, the new Prayer Book and the Act of Uniformity.

The preamble of the Act recites that the king had of late set forth and established by authority of Parliament an order for common prayer in a book entitled, "The Book of Common Prayer and Administration of the Sacraments, and other rites and ceremonies of the Church, after the Church of England". The first section then suppressed and forbade all books or writings in Latin or English used for church services other than such as were appointed by the king's majesty. And all such books were to be collected by the mayor and other civil authorities and delivered to the bishops to be destroyed.

When Somerset was replaced as Protector by John Dudley, soon to be Duke of Northumberland, in 1549, more Protestant reforms were made. The Church hierarchy was altered slightly, with minor orders such as sub-deacon being removed. Altars were replaced with communion tables in the centre of the church rather than in the east end. Some of the more conservative ministers resigned or were deprived in the light of these changes.

But as the "First Prayer-book" of Edward VI did not satisfy the reformers, it was soon supplanted by the "Second Prayer-book", issued in 1552 and also sanctioned by Act of Parliament. This Act of Uniformity is the first to be expressly called by that name, being entitled "An Act for the Uniformity of Service and Administration of Sacraments throughout the realm". It goes much further than the previous Act, for it enforces church attendance on Sundays and holy days. After the preamble declaring the desirability of uniformity, the second section enacted that after November 1, 1552, all persons had to attend their parish church on Sundays and holy days and had to be present at the common prayer, preaching, or other service, under pain of punishment by the censures of the Church. The archbishops and bishops were charged with the task of enforcing the Act and inflicting the censures of the Church on offenders. The fifth section referred to the new "Book of Common Prayer", to which had been added a "Form and Manner of making and consecrating archbishops, bishops, priests, and deacons", and declared that all the provisions of the previous Act shall apply to it. By the sixth and last section, any person convicted of being present at any other form of common prayer or administration of the sacraments would be imprisoned for six months for the first offence, one year for the second, and shall suffer imprisonment for life for the third. The Act was to be read in church four times during the following year and once a year afterwards.

The second Prayer Book was more blatantly Protestant than the first. It re-named services that retained their Catholic names such as "matins", which became "morning prayer". More important was its implication for the communion. It was re-named "Lord's Supper" or "Holy Eucharist", and the wording of the ceremony was changed to effectively reject the Catholic belief in transubstantiation. Also, the priests clothes were changed. Cranmer's Forty Two articles were adopted, which gave a clear Protestant interpretation of the Christian religion and eliminated the ambiguities of the Henrician religious settlement.

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