On the outbreak of the English Civil War he joined the army and became captain in Colonel Harley's regiment of the New Model Army in 1645.

He was a member of the deputation which on 6 July 1647 brought up the charge against the eleven Presbyterian members. In late 1647 Goffe played a prominent part in the famous debates of the army council at Putney. The contemporary record of the debates clearly reveals his religious and political radicalism. He was active in bringing King Charles I to trial and signed the death warrant. In 1649, he received an honorary M.A. at Oxford.

He distinguished himself at the Battle of Dunbar, commanding a regiment there and at the Battle of Worcester in 1651.