Within a week of the battle Essex made Skippon his Sergeant-Major-General, a post which carried with it the command of the foot and the complicated duty of arranging the line of battle. In 1643 his religious tracts written in the Netherlands were collected and published as "The Christian Centurion", one of many devotional tracts he published for his troops to read. However, his high level of experience meant that Parliament was unwilling to risk him in action early in the war, though he did serve alongside Essex at Gloucester. His first field command came on 20 September 1643, with command of the left wing and reserves at the First Battle of Newbury. He continued serving with Essex during the disastrous Lostwithiel campaign and was left in command of the Parliamentarian garrison of 6,000 there on 1 September 1644 when Essex and Lord Robartes fled to Plymouth. The following day, without hope of reinforcement, Skippon negotiated with King Charles: having gained very reasonable terms for his forces, he surrendered and marched his force out of the town. He then gathered the infantrymen from that force in October and marched them to take part in the second Battle of Newbury, occupying the centre of the high ground near Stockcross and recapturing seven of the guns they had lost at Lostwithiel.