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He wrote many books like The History of the Holy War (1639), The Holy State and Profane State (1642), Good Thoughts in Bad Times (1645), Good Thoughts in Worse Times (1647), A History of the University of Cambridge (1659) and Mixed Contemplations in Better Times (1660).
Thomas Fuller strongly supported the English Royalist party and was very loyal to King Charles I of England. He suffered a lot after his defeat but later on, after the English Restoration, he became Chaplain to King Charles II of England.