At the outbreak of the First English Civil War he took sides with the parliament, and was appointed to preach the fast sermon on 22 February 1643.
In the preface to a short work ‘The Pastor and the Clerk; or a Debate (real) concerning Infant-Baptisme,’ published in June of that year, he regretted his contributions to the recent turmoil and the publication of Vindiciæ Catholicæ.
He was allowed to retain his living at the Restoration, and was presented by the king to the first and second portions of Waddesdon, 24 October and 8 November 1661, thus becoming sole rector.
Ellis was strongly attacked, especially by Henry Hickman in his ‘Apologia pro Ministris in Anglia (vulgo) Non-conformists,’ 1664.
Ellis died at Waddesdon on 3 November 1681, aged 75, and was buried on the 8th in the north side of the chancel of the church, within the altar rails.