The King created him a baronet in August 1641, hoping to gain his support, but Mauleverer supported Parliament during the English Civil War and raised a regiment of foot and a troop of horse for Parliament out of his own pocket – for which he later claimed £15,000 reimbursement.
When the Royalists marched to besiege Hull, Fairfax commissioned Mauleverer to seek out spies and traitors in the town.
He accompanied Sir Thomas Fairfax to the relief of Nantwich in January 1644, but while he was on campaign, his ancestral estate at Allerton Mauleverer was plundered by Royalists.
Mauleverer was appointed a commissioner of the High Court of Justice in January 1649, and was a signatory of the King's death warrant.
His son and heir Sir Richard Mauleverer had fought for the Royalists, so was allowed to succeed to the baronetcy after the Restoration.