Burges was also convener of one of the three committees into which the assembly divided itself at the beginning of its work. His liturgical knowledge (he had a fine collection of the various issues of the common prayer-book) may be traced, Alexander Ferrier Mitchell thinks, in the composition of the 'Directory'. Burges was one of the few who, in 1643, opposed the imposition of the Solemn League and Covenant, and he carried his opposition so far as to petition the House of Commons to be heard against it. He was not anxious to create an irreparable breach with the episcopal party. John Lightfoot on this occasion abused Burges as 'a wretch to be branded to all posterity, seeking for some devilish ends, either of his own or others, or both, to hinder so great a good of the two nations'. The commons on 2 September suspended Burges from the assembly as a 'turbulent doctor', and would not readmit him till on 15 September he had made his humble apology. However, the covenant was not signed until a clause had been inserted, limiting the sort of 'prelacy' against which it was aimed, so that the 'advocates of a reformed episcopacy could swallow it'. Having once taken the covenant, Burges revered its binding obligation, and could never be prevailed upon to renounce it. Four shillings a day was assigned by the ordinance to each assembly-man; but the allowance was paid in irregular driblets, and Burges was one of those who declined their share, that the poorer members might come somewhat better off. On 12 March 1644 he was appointed (on the petition of the common councillors of London, December 1643) lecturer at St.Paul's, with a pension of £400 a year, and the dean's house as a residence. On 6 February 1645 he was ordered to give up Watford and Philip Goodwin succeeded him. Later Burges was to shift positions. Around 1645-6, according to Trevor-Roper, the new kind of radical preacher exemplified by Hugh Peter becomes prominent, and Burges was in the group dropping away from the close supporters of Oliver Cromwell. He joined the Presbyterian wing of the opposition. The "Vindication of the Ministers of the Gospel in and about London" was drawn up by Burges in January 1649, and subscribed to by fifty-six other ministers who followed his lead. When King Charles was brought to trial, Burges was the foremost, at great personal risk, in protesting against the proceeding with his usual freedom and vigour.