Larkham's conduct in taking on civil as well as religious authority led to much discontent and even open warfare, and commissioners from Boston, of whom Hugh Peters was one, were sent to arbitrate.

The vicarage of St Eustachius' Church, Tavistock had been vacant since George Hughes accepted a call from the people of Plymouth on 21 October 1643.

According to the report of the commissioners, who, under the Act for Providing Maintenance for Preaching Ministers, visited Tavistock on 18 October 1650, Larkham was elected by the inhabitants, and presented by the Earl of Bedford.

On 15 November 1649 he had been dismissed from his post as chaplain of Waller's regiment, 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; and on 11 June 1652 pay from Ebthery at Bristol.

He had in the pulpit spoken against neighbouring ministers and John Howe, then of Great Torrington, openly protested against one of Larkham's sermons, which was afterwards published in his Attributes of God, 1656.

Larkham resisted the arrangement, but the council of state ordered the justices living near Tavistock (17 March 1659–60) to take measures to continue the lectures, and to examine witnesses.

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 Mile Act.

Regrettably, records from the 1600s remain scarce, but possibly, more will be recovered since Dr. Susan Moore has published her edition, with extra materials, of Larkham's Daily Journal, his Diary.