Cotton supported the claim of King James VI of Scotland to succeed Queen Elizabeth I on the English throne, and after the queen's death was commissioned to write a work defending James's claim to the throne, for which he was rewarded with a knighthood in 1603. Cotton was elected to parliament for Huntingdonshire in 1604, a constituency previously represented by his grandfather. Cotton worked on the Committee on Grievances and in 1605–06 received the Bill pertaining to the Gunpowder Plot through his work on the Committee of Privileges. In 1607 he was reappointed to the Committee of Privileges. Cotton was appointed to the joint conference with the Lords during his work on the bill pertaining to the full union between Scotland and England in 1606–07. In 1610 Cotton was nominated in first place to the Committee of Privileges. In 1610/11 the royal revenues were low, and Cotton wrote "Means for raising the king’s estate." In this work he suggested the formation of the baronetcy, a new higher order of social rank, higher than the knight but lower than the baron.