In the second parliament there was not so much scope for the exercise of his powers. The Gunpowder Plot had aroused in the Commons warmer feelings towards the king; they passed severe laws against recusants, and granted a triple subsidy. At the same time they continued the collection of the grievances concerning which they were to move. In the course of this session Bacon married Alice Barnham "the alderman's daughter, an handsome maiden, to my liking," of whom he had written some years before to his cousin Cecil. Little or nothing is known of their married life.

The third parliament was chiefly occupied with the commercial and legal questions rising out of the proposed Union, in particular, with the dispute as to the naturalization of the Post Nati. Bacon argued ably in favour of this measure, but the general feeling was against it. The House would only pass a bill abolishing hostile laws between the kingdoms; but the case of the Post Nati, being brought before the law courts, was settled as the king wished. Bacon's services were rewarded in June 1607 by the office of solicitor.[8] Several years passed before he gained another step. Meantime, though circumstances had thrown him too much into active life, he had not forgotten his cherished project of reorganizing natural science. A survey of the ground had been made in the Advancement, and some short pieces not published at the time were probably written in the subsequent two or three years. Towards the close of 1607 he sent to his friends a small tract, entitled Cogitata et Visa, probably the first draft of what we have under that title.

In 1609 he wrote the noble panegyric, In felicem memoriam Elizabethae, and the curiously learned and ingenious work, De Sapientia Veterum; and completed what seems to have been the Redargutio Philosophiarum, or treatise on the "idols of the theatre."

In 1610 the famous fourth parliament of James met. Prerogative, despite Bacon's advice and efforts, clashed more than once with liberty; Salisbury's bold schemes for relieving the embarrassment caused by the reckless extravagance of the king proved abortive, and the House was dissolved in February 1611. Bacon took a considerable share in the debates, consistently upheld the prerogative, and seemed yet to possess the confidence of the Commons. The death of Salisbury, occurring soon after, opened a position in which Bacon thought his great political skill and sagacity might be made more immediately available for the king's service. How far he directly offered himself for the post of secretary is uncertain, but we know that his hopes were disappointed, the king himself undertaking the duties of the office. About the same time he made two ineffectual applications for the mastership of the wards; the first, on Salisbury's death, when it was given to Sir George Carey; the second, on the death of Carey. It is somewhat hard to understand why so little favour was shown by the king to one who had proved himself able and willing to do good service, and who, in spite of his disappointments, still continued zealously to offer advice and assistance.

At last in 1613, a fair opportunity for promotion occurred. The death of Sir Thomas Fleming made a vacancy in the chief justiceship of the king's bench, and Bacon, after some deliberation, proposed to the king that Coke should be removed from his place in the court of common pleas and transferred to the king's bench. He gives several reasons for this in his letter to the king, but in all probability his chief motive was that pointed out by Spedding, that in the court of king's bench there would be less danger of Coke coming into collision with the king on questions of prerogative, in handling which Bacon was always very circumspect and tender. The vacancy caused by Coke's promotion was then filled up by Hobart, and Bacon, finally, stepped into the place of attorney-general. The fact of this advice being offered and followed in all essentials, illustrates very clearly the close relations between the king and Bacon, who had become a confidential adviser on most occasions of difficulty. That his adherence to the royal party was already noticed and commented on appears from the significant remark of Chamberlain, who, after mentioning the recent changes among the law officials, says, "There is a strong apprehension that ... Bacon may prove a dangerous instrument."

Further light is thrown upon Bacon's relations with James, and upon his political sympathies, by the letter to the king advocating the calling of a parliament,[9] and by the two papers of notes on which his letter was founded.[10] These documents, even after due weight is given to all considerations urged in their favour,[11] seem to confirm the view already taken of Bacon's theory of government, and at the same time show that his sympathies with the royal party tended to blind him to the true character of certain courses of action, which can only be justified by a straining of political ethics. The advice he offered, in all sincerity, was most prudent and sagacious, and might have been successfully carried out by a man of Bacon's tact and skill; but it was intensely one-sided, and exhibited a curious want of appreciation of what was even then beginning to be looked on as the true relation of king, parliament and people. Unfortunately for James, he could neither adopt nor carry out Bacon's policy. The parliament which met in April 1614, in which Bacon sat for Cambridge University, and was dissolved in June, after a stormy session, was by no means in a frame of mind suitable for the king's purposes.

The House was enraged at the supposed project (then much misunderstood) of the "Undertakers"; objection was taken to Bacon being elected or serving as a member while holding office as attorney-general; and, though an exception was made in his favour, it was resolved that no attorney-general should in future be eligible for a seat in parliament. No supply was granted, and the king's necessities were increased instead of diminished. The emergency suggested to some of the bishops the idea of a voluntary contribution, which was eagerly taken up by the noblemen and crown officials. The scheme was afterwards extended so as to take in the whole kingdom, but lost something of its voluntary character, and the means taken to raise the money, which were not what Bacon would have recommended,[12] were calculated to stir up discontent. The general dissatisfaction received a somewhat unguarded and intemperate expression in a letter sent to the justices of Marlborough by a gentleman of the neighbourhood, named Oliver St John,[13] in which he denounced the attempt to raise funds in this way as contrary to law, reason and religion, as constituting in the king personally an act of perjury, involving in the same crime those who contributed, and thereby subjecting all parties to the curses levelled by the church at such offences.