When Elizabeth became queen in the November of 1558, it was widely believed that she would restore the Protestant faith in England. Although she had adhered to the Catholic faith during her sister's reign, she had been raised a Protestant, and was committed to that faith. Elizabeth's religious views were remarkably tolerant for the age in which she lived. "There is only one Christ, Jesus, one faith," she exclaimed later in her reign, "all else is a dispute over trifles." She also declared that she had "no desire to make windows into men's souls".

Elizabeth had her own private chapel in most of her palaces, and reputedly prayed there everyday. She saw herself as God's vessel on earth, and would pray to determine God's will so that he would reveal it to her, and she could implement it. Although Elizabeth's actual beliefs elude us, we are able to get an indication of them from her attitudes and gestures. Her chapels were conservative; the crucifix was displayed, and she also liked candles and music. She disliked long Protestant sermons, but also expressed displeasure at some Catholic rituals such as the elevation of the host, which implied that she rejected the Catholic belief of transubstantiation. She also did not really approve of the clergy marrying as she expressed on several occasions, but as this was an integral aspect of Protestantism, she had to accept it. A more personal indication of her beliefs are the prayers she wrote for her people, and the letters she wrote to her friends and relations. In these letters she often referred to God and the need to accept his will. In her prayers she also acknowledged her own faults and shortcomings. Elizabeth was by no means the perfect Protestant by the standards of many of her clergy; she swore terribly, using expressions that some thought were blasphemous, one of her favorite being "God's Death", and her sumptuous appearance was criticized by the more radical Protestants, who accused her of vanity and idolatry.

It was the Act of Supremacy that gave Elizabeth ultimate control of the Church of England. In the reign of her father and brother, the monarch had been "Head of the Church in England", but under Elizabeth, this was modified to "Supreme Governor of the Church in England". The change may have been made to appease Catholics who could not accept the monarch as "Head of the Church", seeing the church as the Pope's domain, or it may have been made because Elizabeth was a woman. In the sixteenth century, women were regarded as inferior to men in spiritual matters, and many were uncomfortable with the idea of a woman being in charge. This act also included an oath of loyalty to the queen that the clergy were expected to take. If they did not take it, then they would lose their office. A High Commission was established to ensure that such oaths were taken.

This was the crux of the Elizabethan Church, establishing a set form of worship. The prayer books of Edward VI were fused into one, and were to be used in every church in the land. Church attendance on Sundays and holy days was made compulsory, with a twelve pence fine to be collected if people did not attend, the money to be given to the poor. The wording of the Communion was to be vague so that Protestants and Catholics could both participate, and the ornaments and vestments of the Church were to be retained as they had been before the reforms in the second-year of Edward's reign. Although the passage of the Act of Supremacy through Parliament had been relatively easy, passing the Act of Uniformity was much more difficult. A large number of the Parliament, who were still Catholic, opposed the bill, and it was eventually only passed by three votes. The religious settlement began to be implemented in the summer of 1559.

Catholics did not have an easy time during the reign of Elizabeth, but many of them would have agreed that things could have been much worse. Catholicism was effectively illegal, but it was for not attending church that Catholics were fined, not for simply being Catholic, and the fine applied to dissenting Puritans as well as to those of the Catholic faith. Attendance at mass was to be punished by a fine of 100 marks, but the saying of mass, or arranging for it to be said, carried the death penalty, although Elizabeth ensured that this was never implemented before 1577 as she disliked such extremism. As far as Elizabeth was concerned, so long as Catholics behaved themselves, were loyal to her, and attended church now and then, they were free to believe what they wished. Elizabeth tried to accommodate Catholic beliefs in her religious settlement so that they could go to church without feeling guilty or disloyal to their faith, and often turned a blind eye to Catholics who had secret services in their home. There was no attempt to ruthlessly seek out Catholics, and no desire to put ordinary men and women to death simply for their faith.

It was only as the Catholic threat against Elizabeth from Europe heightened as the reign progressed, that the Elizabethan government had to take a harsher stance against Catholics than they had initially anticipated. Some of Elizabeth's ministers, such as Sir Francis Walsingham, were zealously committed to the Protestant cause and wished to persecute Catholics in England, but their ambitions were always held in check by the queen. For the first decade of the reign, the Catholics suffered little.

It was not until the Papal Bull of 1570 that the situation changed. The new pope, Pius V, did not like Elizabeth, and like all Catholics, believed that she was illegitimate, and thus had no right to the throne of England. Catholics believed that the true queen of the land was Mary Queen of Scots. In 1570 he issued a bull, "Regnans in Excelsis", against Elizabeth, that excommunicated her and absolved all her subjects from allegiance to her and her laws. This was a drastic step, and one that was not approved of by Philip II of Spain, or some English Catholics, who knew that this would make things difficult for Catholics in England. Excommunication was a great disgrace to Catholics. An excommunicated person was not to be dealt with, as it was believed that they were unchristian and would go to hell. The excommunication of Elizabeth must have been a very painful experience for her Catholic subjects. They were cruelly torn between two loyalties; loyalty to the queen many of them respected, if not loved, and loyalty to the Pope, who they believed was God's representative on Earth. Many Catholics probably never solved the dilemma, ignored it, or remained loyal to both, separating their spiritual and secular allegiances.

From this moment on, Catholics were seen as a great threat to the queen and the realm. The plots against Elizabeth's life that occurred from the 1570's onwards also did much to fossil the idea that Catholics were traitors, as did the continuous flow of Jesuit priests into the country. The entrance of Jesuits into the country was prohibited by law in 1585, but still they came in the hope of converting the English population to Catholicism. It was these who bore the brunt of the Catholic persecution. Many of them were executed for treason. William Cecil devised questions to be asked of English Jesuits and Priests, and the question over who they would support if the Pope invaded the country, Pope or Queen, was their down fall every time. This question became known as it is still known today, "The bloody question", as there was really only one answer that a true Catholic could give.

In 1581 an Act was passed that made it treason to withdraw English subjects from allegiance to the Queen or her Church, and fines for recusancy (refusing to go to church) were increased to twenty pounds - a phenomenal amount to the Elizabethans, considering that the annual income of a knight would only be about fifty pounds. The Elizabethan government genuinely believed that Catholics, particularly the Jesuits, posed a serious threat to the Queen's life and reign, and the literature produced by the leaders of the "English Mission", an active campaign to restore Catholicism in the land and depose Elizabeth, seemed to confirm their suspicions.

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