The rectory of Broadwindsor, Dorset, then in the diocese of Bristol, was his next preferment (1634); and on 11 June 1635 he achieved the degree of Bachelor of Divinity from Sidney Sussex College, Cambridge.

At Broadwindsor, early in 1641, Thomas Fuller, his curate Henry Sanders, the churchwardens, and five others certified that their parish, represented by 242 adult males, had taken the Protestation ordered by the speaker of the Long Parliament.

Fuller was not formally dispossessed of his living and prebend on the triumph of the Presbyterian party, but he relinquished both preferments about this time.

In one he set forth with searching and truthful minuteness the hindrances to peace, and urged the signing of petitions to the king at Oxford, and to the parliament, to continue their care in advancing an accommodation.

[4] When it was expected, three months later, that a favourable result would attend the negotiations at Oxford, Fuller preached a sermon at Westminster Abbey, on 27 March 1643, on the anniversary of Charles I's accession, on the text, "Yea, let him take all, so my Lord the King return in peace."

He was now obliged to leave London, and in August 1643 he joined the king at Oxford, where he lodged in a chamber at Lincoln College.

Fuller subsequently published by royal request a sermon preached on 10 May 1644, at St Mary's, Oxford, before the king and Prince Charles, called Jacob's Vow.

For the first five years of the war, he "had little list or leisure to write, fearing to be made a history, and shifting daily for my safety.

Under the Articles of Surrender Fuller made his composition with the government at London, his "delinquency" being that he had been present in the king's garrisons.

In Andronicus, or the Unfortunate Politician (1646), partly authentic and partly fictitious, he satirised the leaders of the Revolution; and for the comfort of sufferers by the war he issued (1647) a second devotional manual, entitled Good Thoughts in Worse Times, abounding in fervent aspirations, and drawing moral lessons in beautiful language out of the events of his life or the circumstances of the time.

In grief over his losses, which included his library and manuscripts (his "upper and nether millstone"), and over the calamities of the country, he wrote his work on the Cause and Cure of a Wounded Conscience (1647).

It was prepared at Boughton House in his native county, where he and his son were entertained by Edward Lord Montagu, who had been one of his contemporaries at the university and had taken the side of the parliament.

At Chelsea, where he also occasionally officiated, he covertly preached a sermon on the death of Charles, but he did not break with his Roundhead patrons.

His possession of the living was in jeopardy on the appointment of Oliver Cromwell's "Tryers"; but he evaded their inquisitorial questions by his ready wit.

A Panegyrick to His Majesty on his Happy Return, one of the many contemporary poems celebrating the restoration of Charles II, was the last of Fuller's verse efforts.

He resumed his lectures at the Savoy, where Samuel Pepys heard him preach; but he preferred his conversation or his books to his sermons.