Manaton was next elected as MP for Launceston in April 1640 for the Short Parliament. He was re-elected in November 1640 for the Long Parliament and sat until 1641 when he was disabled for supporting King Charles I.[3] Manaton was created D.C.L. at the University of Oxford on 21 March 1644.[2] He entertained King Charles at his house in 1644.[4]
Manaton died in 1651[5] and was buried at South Petherwin, where his monument displayed the arms of Manaton and Reskymer, and Manaton and Edgcombe.[4]
Manaton married as his second wife Jane Mapowder daughter of Narcissus Mapowder of Holsworthy, Devon. Their sons Ambrose and Henry were both subsequently Members of Parliament.[6]