Mather enumerates him among 'godly anabaptists;' the date of his adoption of this type of doctrine and practice is not clear.
On 24 Dec. 1641 he reached London on his return to this country at the instance of his aged father, He opened a boarding-school on Great Tower Hill. Soon afterwards he was elected to the mastership of the free school in the parish of St. Mary Axe. As a schoolmaster he was very successful, but after holding this office for about a year he gave it up to become an army chaplain. Dissatisfied with the spirit of the parliamentary commanders, he returned to London and to school-keeping. He learned Hebrew from Christian Ravy [Ravis] Berlinas, 'Hebrew professor' in London. In 1644 we find him preaching in London and Suffolk churches and churchyards, and occasionally, in what afterwards became quaker fashion, endeavouring to supplement the regular sermon by a discourse of his own. This led, according to Edwards (Gangraena, 2nd ed. 1646, i. 129 sq.), to 'riots and tumults' for which Knollys was twice brought before a committee of parliament, but on each occasion 'got off.' In fact he was absolved from blame and protected in his action. He gathered a church of his own in 1646, meeting first for about a year, in Great St. Helen's, 'next door to the publique church,' then in Finsbury Fields, next in Coleman Street, subsequently in George Yard, Whitechapel, and ultimately at Broken Wharf, Thames Street. His most important convert was Henry Jessey [q. v.], whom he baptised in June 1645. A letter (11 Jan. 1646) from him to John Dutton of Norwich, in favour of toleration, printed by Edwards (ib, iii. 48), embittered the presbyterians against him. But his ministry was popular; though Edwards calls him 'a weak man, and a sorry disputant,' he attracted nearly a thousand hearers. He subscribed the second edition (1646) of the confession of faith issued by London baptists, but not the original edition (1644). On 17 Jan. 1649 parliament gave a commission to him and William Kiffin [q. v.] to preach in Suffolk, on petition from inhabitants of Ipswich. His name is attached to pleas for toleration addressed to parliament in 1651 and 1654, and to the lord protector on 3 April 1657.
Between 1645 and the Restoration Knollys met with no interference. He held some offices of profit under Cromwell's government, resigning on 29 March 1653 the post of examiner at the customs and excise, with a salary of 120l., 'for more beneficial employment.' He was clerk of the check till 23 May 1655. On the outbreak (7 Jan. 1661) of Venner's insurrection he was committed to Newgate on groundless suspicion, and detained till the act of grace on the king's coronation (23 April) liberated him. It was not safe for him to resume his ministry in London; he made some stay in Wales, and twice sought a refuge in Lincolnshire. Sailing thence for Holland, he made his way to Germany, where he remained two or three years, returning at length to London by way of Rotterdam. In his absence, Colonel Legge, lieutenant of the ordnance, in the king's name took forcible possession of his property (a house and garden worth 700l, and 200l. deposited with the Weavers' Company).
In London he once more resumed his school and his pastorate, preaching also a morning lecture on Sundays at Pinners' Hall, Old Broad Street, then in the hands of independents. On 10 May 1670 he was arrested at his meeting in George Yard, under the second Conventicle Act, which had just come into force. He was committed to the Bishopgate compter, but was considerately treated and was allowed to preach to the prisoners; at the next Old Bailey sessions he obtained his discharge. He survived the Toleration Act, and, though in extreme old age, took a leading' part in efforts made in 1689 for the consolidation of the baptist cause. He retained great vigour both of body and mind; when attacked by illness he discarded medicine, and resorted to anointing and prayer. He continued preaching to the last, when he could scarcely stand or make his voice heard. Robert Steed was his assistant.
He died on 19 Sept. 1691, in his ninety-third year, and was buried in Bunhill Fields. The funeral sermon was preached by Thomas Harrison (1699-1702), particular baptist minister at Petty France, and afterwards at Loriners' Hall. His portrait, at the age of sixty-seven, was engraved; the print, as reproduced by Hopwood, is given in Wilson. An engraving by van Hove, representing him in his ninety-third year, is prefixed to his 'Life.' He wore long hair, mostly covered by a loose skull-cap, and no beard. He married in 1630 or 1631; his wife died on 30 April 1671; he had at least three sons and a daughter; Isaac, his last surviving son, died on 16 Nov. 1671.
He published: 1. 'A Glimpse of Sion's Glory,' &c., 1641, 4to (this is probably his), 2. 'A Modest Answer to Dr. Bastwick's book called "Independency not God's Ordinance,' &c., 1645, 4to. 3. 'Christ Exalted . . . sermon . . . at Debenham [Coloss. iii. 11], another sermon [Ephes. i. 4],'&c., 1645, 4to; 2nd ed. 1645, 4to. 4. 'The Shining
