1649 he had been dismissed from his post as chaplain of Waller's regiment. According to his 'Diary' he had had 'differences about their irreligious carriage.' But he really seems to have been dismissed after a court-martial, which sat for two days at Plymouth, had found him guilty of inciting to insubordination. He seems nevertheless to have secured some other military post, for he speaks of receiving money in 1651 at a 'muster in Carlisle for my men;' and on 11 June 1652 he received eleven days' pay from Ebthery at Bristol, 'they being about to take ship,' for Ireland probably. He was thus absent from Tavistock almost the whole of 1651–2, and owing to his absence, and to his introduction after his return of novelties in the church, 'which would have wearied any but an Athenian Spirit,' his congregation showed much discontent. In 1657 Larkham attacked his chief enemies in a tract entitled 'Naboth, in a Narrative and Complaint of the Church of God at Tavistock, and especially of and concerning Mr. Thomas Larkham.' Five leading parishioners, who were especially abused, replied in 'The Tavistock Naboth proved Nabal: an Answer to a Scandalous Narrative by Thomas Larkham, in the name, but without the consent, of the Church of Tavistocke in Devon, etc., by F. G., D. P., W. G., N. W., W. H., etc.,' 4to, London, 1658 (Bodleian). Larkham in his 'Diary' calls this reply 'a heape of trash, full fraught with lies and slanders,' but the authors seem to have been justified in their denunciations of Larkham's affection for sack and bowls, which his 'Diary' corroborates. They also allude to his published attacks on tithes, although his 'Diary' proves that he made every effort to exact the Lamerton tithes from refractory farmers. Accusations of immorality in New England and at home had, it was further declared, been brought against him by one of the commissioners. Larkham retorted in a pamphlet called 'Judas Hanging Himself,' which is no longer extant, and his enemies answered him again in 'A Strange Metamorphosis in Tavistock, or the Nabal-Naboth improved a Judas,' &c., 4to, London, 1658, British Museum. But Larkham, who was 'out in printing Naboth 1l. 10s.' (Diary, October 1657), allowed the controversy to drop there. Already he had in the pulpit spoken of the neighbouring ministers as 'doing journey work,' and had asserted that 'many of them would sooner turn Presbyterians, Independents, nay Papists, rather than lose their benefices.' The celebrated John Howe, then of Great Torrington, openly protested against one of Larkham's sermons, which was afterwards published in his 'Attributes of God,' 1656.
In October 1659, to Larkham's disgust, a weekly lecture was established in Tavistock by his opponents, and the neighbouring ministers officiated. Larkham resisted the arrangement, but the council of state (State Papers, Dom. cxx. 226) ordered the justices living near Tavistock (17 March 1659–60) to take measures to continue the lectures, and to examine witnesses as to the 'crimes and misdemeanors' alleged against Larkham. The charges chiefly consisted of expressions he had used in sermons, in derogation of the restored Long parliament, and in contempt of Monck. The justices sat to hear evidence on 17 April, and Larkham was ordered to admit others to preach in the parish church. On 19 Oct. the justices met to consider whether he had been legally appointed to the vicarage of Tavistock, and he was bound over to appear at the Exeter assizes. On Sunday the 21st Larkham, in compliance with the Earl of Bedford's desire, resigned the benefice. He was nevertheless arrested on 18 Jan. 1660–1, and spent eighty-four days in prison at Exeter. On his release he returned to Tavistock, living with his son-in-law, Condy, and preaching occasionally in retired places, but left the town on being warned of impending prosecutions under the Five Miles Act. In 1664 he became partner with Mr. County, an apothecary in Tavistock, and carried on the business successfully after Mr. County's death. The last entry in his 'Diary' is dated 17 Nov. 1669, and he was buried at Tavistock on 23 Dec.
On 22 June 1622 he married Patience, daughter of George Wilton, schoolmaster, of Crediton. Of this marriage were born four children: Thomas, died in the West Indies, 1648; George, went to Oxford and became minister of Cockermouth; Patience, married Lieutenant Miller, who died in Ireland, 1656; and Jane, married Daniel Condy of Tavistock.
His works are, besides the tracts already mentioned:
- 'The Wedding Supper,' 12mo, London, 1652, with portrait, engraved by T. Cross. Dedicated to the parliament.
- 'A Discourse of Paying of Tithes by T. L., M.A., Pastour of the Church of Tavistocke,' 12mo, London, 1656. Dedicated to Oliver Cromwell.
- 'The Attributes of God,' &c., 4to, London, 1656, with portrait, British Museum. Dedicated to the fellows, masters, and presidents of colleges, &c., at Cambridge.
All his works are very scarce, especially the tracts. His manuscript 'Diary' from 1650 to 1669 has been edited, but much abbreviated and expurgated, by the Rev. W. Lewis.