On the surrender of Reading (26 April 1643), Thomas Bunbury, vicar of St. Mary's, joined King Charles in Oxford; his living was sequestered and given to Fowler.
Thinking himself unsafe in the neighbourhood of the royalist troops at Donnington Castle in Berkshire, garrisoned for the king at the time of the second battle of Newbury (27 October 1644), Fowler went to London.
In this capacity he was mixed up with the proceedings against John Pordage, formerly of St Laurence's Church, Reading, whom the commissioners ejected (by order 8 December 1654, to take effect 2 February 1655) from the rectory of Bradfield, Berkshire.
Fowler wrote an account and defence of this business, in which he and John Tickel, presbyterian minister at Abingdon, had taken a leading part.
With Simon Ford, vicar of St. Laurence's, Reading, he published (1656) an answer to the 'quaking doctrines' of Thomas Speed of Bristol; and he engaged in controversy (1659) with Edward Burrough.
On the restoration of the monarchy Fowler lost his fellowship at Eton, but retained the Reading vicarage till he was ejected by the Act of Uniformity 1662.