His sympathies were with the fringe Independent sects of the Commonwealth period, and after the English Restoration of 1660 his life was embattled.
[2][3] A position teaching at Westminster School in 1656 ended badly when he quarreled with headmaster Richard Busby.
A large and acrimonious pamphlet literature grew up around Bagshaw, some of it generated by his hostility to George Morley, the Restoration bishop of Worcester (translated in 1662 to Winchester), and Dean of Christ Church from 1660.
To the end he was also arguing out the separatist case against Richard Baxter, who hoped to keep dissenters (apart from the extremes) within the Church of England.
[8] In 1672, Baxter was still accusing Bagshaw of tricky polemics, in trying to draw discussion of the position of honest Nonconformist dissenters onto the touchy grounds of full toleration, politics and war.