In this role, Berry's sympathetic treatment of Fifth Monarchists and Quakers, two religious sects many viewed as anarchic revolutionaries, meant he was seen as unreliable by George Monck, architect of the 1660 Stuart Restoration.

[a] His friend Baxter, who was viewed as a moderate Presbyterian, reportedly refused an invitation to serve the Ironsides as chaplain, allegedly due to his dislike of their religious radicalism.

[8] After the New Model Army was formed in April 1645, Berry and his troop became part of Sir Thomas Fairfax' regiment, which was present at Naseby, Langport, and the storming of Bristol in September 1645.

[10] However, victory resulted in bitter disputes over the post-war political settlement between the New Model Army, led by Fairfax and Cromwell, and the majority of MPs in Parliament.

Berry served with the forces sent north to deal with an invading army of Scots supported by their English allies, and fought at the Battle of Preston in August, a victory which ended serious Royalist resistance.