James I had assumed that all religious issues had been solved by the Hampton Court Conference and that the Church would suitably advance in a modern state that would reflect well on his kingdom. However, the conference at Hampton Court threw up as many issues as it solved and the whole issue of conformity continued to dog James who found that the Puritans had many supporters in both Houses of Parliament.
In September 1604 a definitive code of canons was produced. This required all ministers to subscribe to three articles. The first affirmed royal supremacy and caused no problems. The third article stated that all Thirty-Nine Articles were agreeable to the 'Word of God' and this was more contentious. However, the second article caused a great deal of unhappiness amongst Puritans. The second article stated that the Book of Common Prayer “containeth in it nothing contrary to word of God” and required all ministers to only use the authorised services. Those Puritans who leaned towards the radical element as opposed to the likes of the moderate John Reynolds who represented the Puritans at the Hampton Court Conference, could not accept this as they felt that there were too many 'popish' elements in the Prayer Book.
The first Parliament of James's reign met in March 1604. It soon became clear that the Puritans had many supporters in the House of Commons who were willing to speak out on their behalf. Many MP's made it clear that the issue of 'popish' clothing being worn and the threat of ministers being dismissed if they did not conform were unacceptable and they partitioned James accordingly. James was not impressed as he believed that the Hampton Court Conference had answered all their problems. James was already at odds with Parliament over its failure to support him over his plans for a statutory union between England and Scotland, so this was not the most auspicious start to the relationship between the new Stuart king and Parliament. In July 1604, James reaffirmed his belief that the Book of Common Prayer should remain as it was and that the arguments presented by certain elements in Parliament were not sustainable. James also publicly stated that he believed that there were those in Parliament who were seeking to cause trouble as opposed to seeking harmony.
In the House of Commons Sir Francis Hastings took up the cause of the Puritans. The Commons established a committee to examine religious issues that were causing concern. James asked that the committee should confer with the Convocation. However, the Commons considered this to be an inferior body to a parliamentary committee and saw no reason why it should do this. However, in a gesture of conciliation, the committee did agree to meet with the bishops in the House of Lords.
The committee's report contained issues that would have pleased James. The Commons wanted an educated clergy that could administer to the needs of a parish and it wanted an end to pluralism. But the committee avoided the issue of how this could be funded. However, this had already been discussed at Hampton Court. The committee also stated that no minister should be “deprived, suspended, silenced or imprisoned” if he failed to conform to the Thirty Nine Articles.
The approach of the Commons was clearly seen in June 1604. A bill was drafted that wanted all those land owners who had gained former Church land to hand over part of their annual income from this land to fund the eradication of pluralism and the education and maintenance of the clergy. The bill was promptly rejected.
The stance of Parliament seems to have made James even more determined to enforce what was decided at Hampton Court. In July 1604, he made it clear that he would use the law to enforce his policies if he had to. This did nothing to end the Puritans campaign. In the winter of 1604, James went hunting. At Royston, he was approached by 27 Puritans who presented him with a petition regarding what they wanted. He ordered that the “disorderly” group had to immediately leave his presence. He openly criticised the bishops for not putting into practice what had been decided at Hampton Court - effectively accusing them of being lazy - and ordered Richard Bancroft to start enforcing religious law as it stood.
The bishops started a campaign to bring round the clergy to accept what James wanted. To all intents they were successful as the government claimed that only ninety clergy were ever deprived of their living and these were seen as being the ones who refused to even consider changing their approach. Many non-conformist ministers continued with their work but were diplomatic in their approach and did not bring attention to themselves. The Puritans claimed 300 Puritan ministers were dismissed but the records do not support this figure - though the government did control record keeping. If 300 was an accurate figure, it represented just 3% of the overall number of clergy at the time. The government figure of 90 would represent about 1% of the total. Those that replaced the dismissed clergy were moderates who outwardly conformed and it does seem that the approach that James took only removed the hard-liners who were not willing to change their beliefs or their approach.