Between 1654 and 1657 he was repeatedly sent to prison for interrupting services, and in 1661 was imprisoned for some religious offence at Leicester.
Most of his time seems to have been spent in preaching excursions, although till 1665 at least he retained his situation at Swarthmore, and in this year he was imprisoned in Lancaster Castle for being at an illegal conventicle.
In the intervals between his imprisonments he was engaged in ministerial work, chiefly in the northern counties and in Wales, and his preaching is said to have been of an earnest and loving character rather than argumentative or doctrinal.
In September 1684 he was sent to gaol for more than a month for absenting himself from the parish church, and immediately after his release was again arrested and incarcerated for about eight weeks for the same offence.
In 1699 Fell went on a preaching tour in northern England, with Benjamin Holme and Joseph Kirkbride.