This prudent advice was unfortunately rejected. But while he went cordially with the king in domestic affairs, he was not quite in harmony with him on questions of foreign policy. Not only was he personally in favour of a war with Spain for the recovery of the Palatinate, but he foresaw in such a course of action the means of drawing together more closely the king and his parliament. He believed that the royal difficulties would be removed if a policy were adopted with which the people could heartily sympathize, and if the king placed himself at the head of his parliament and led them on. But his advice was neglected by the vacillating and peace-loving monarch, his proffered proclamation was put aside, and a weak, featureless production substituted in its place. Nevertheless the new parliament seemed at first more responsive than might have been looked for. A double subsidy was granted, which was expressly stated to be "not on any consideration or condition for or concerning the Palatinate." The session, however, was not far advanced when the question of patents was brought up; a determined attack was made upon the very ones of which Bacon had been in dread, and it was even proposed to proceed against the referees (Bacon and Montagu) who had certified that there was no objection to them in point of law.

This proposal, though pressed by Coke, was allowed to drop; while the king and Buckingham, acting under the advice of Williams, afterwards lord keeper, agreed to give up the monopolies. It was evident, however, that a determined attack was about to be made upon Bacon, and that the proceeding against the referees was really directed against him. It is probable that this charge was dropped because a more powerful weapon had in the meantime been placed in his enemies' hands. This was the accusation of bribery and corrupt dealings in chancery suits, an accusation apparently wholly unexpected by Bacon, and the possibility of which he seems never to have contemplated until it was actually brought against him. At the beginning of the session a committee had been appointed for inquiring into abuses in the courts of justice. Some illegal practices of certain chancery officials had been detected and punished by the court itself, and generally there was a disposition to overhaul its affairs, while Coke and Lionel Cranfield, earl of Middlesex (1575-1645) directly attacked some parts of the chancellor's administration.

But on the 14th of March one Christopher Aubrey appeared at the bar of the House, and charged Bacon with having received from him a sum of money while his suit was going on, and with having afterwards decided against him. Bacon's letter[29] on this occasion is worthy of serious attention; he evidently thought the charge was but part of the deliberate scheme to ruin him which had already been in progress. A second accusation (Edward Egerton's case) followed immediately after, and was investigated by the House, who, satisfied that they had just matter for reprehension, appointed the 19th for a conference with the Lords. On that day Bacon, as he had feared, was too ill to attend. He wrote[30] to the Lords excusing his absence, requesting them to appoint a convenient time for his defence and cross-examination of witnesses, and imploring them not to allow their minds to be prejudiced against him, at the same time declaring that he would not "trick up an innocency with cavillations, but plainly and ingenuously declare what he knew or remembered." The charges rapidly accumulated, but Bacon still looked upon them as party moves, and was in hopes of defending himself.[31] Nor did he seem to have lost his courage, if we are to believe the common reports of the day,[32] though certainly they do not appear worthy of very much credit.

The notes[33] bearing upon the interview which he obtained with the king show that he had begun to see more clearly the nature and extent of the offences with which he was charged, that he now felt it impossible altogether to exculpate himself, and that his hopes were directed towards obtaining some mitigation of his sentence. The long roll of charges made upon the 19th of April finally decided him; he gave up all idea of defence, and wrote to the king begging him to show him favour in this emergency.[34] The next day he sent in a general confession to the Lords,[35] trusting that this would be considered satisfactory. The Lords, however, decided that it was not sufficient as a ground for their censure, and demanded a detailed and particular confession. A list of twenty-eight charges was then sent him, to which an answer by letter was required. On the 30th of April his "confession and humble submission"[36] was handed in. In it, after going over the several instances, he says, "I do again confess, that on the points charged upon me, although they should be taken as myself have declared them, there is a great deal of corruption and neglect; for which I am heartily and penitently sorry, and submit myself to the judgment, grace, and mercy of the court."[37] On the 3rd of May, after considerable discussion, the Lords decided upon the sentence, which was,[38] That he should undergo fine and ransom of £40,000; that he should be imprisoned in the Tower during the king's pleasure; that he should be for ever incapable of any office, place or employment in the state or commonwealth; that he should never sit in parliament, or come within the verge of the court.

This heavy sentence was only partially executed. The fine was in effect remitted by the king; imprisonment in the Tower lasted for about four days; a general pardon (not of course covering the parliamentary censure) was made out, and though delayed at the seal for a time by Lord Keeper Williams, was passed probably in November 1621. The cause of the delay seems to have lain with Buckingham, whose friendship had cooled, and who had taken offence at the fallen chancellor's unwillingness to part with York House. This difference was finally smoothed over, and it was probably through his influence that Bacon received the much-desired permission to come within the verge of the court. He never again sat in parliament.