He enjoyed the patronage of John Lambert, who he served under during the First English Civil War, which helped his parliamentary career, but also later led to his downfall when the Royalists regained power in 1660.
Baynes was moved to London, where he acted as the brigade's financial agent, purchasing lands, soldier's debts and estates for his fellow officers.
[1] He married Martha (née Dawson) in July 1650, and the pair had sixteen children, ten of whom outlived Baynes.
Baynes continued to support Lambert in the House of Commons, opposing the vote to make Richard Cromwell the second Lord Protector.
The dissolution of The Protectorate in 1659 allowed Baynes to return to the Army, but a year later the Royalist favouring Convention Parliament had him arrested and had to forfeit the crown lands he had purchased.