As a royalist, his father left England following the execution of Charles I at the end of the English Civil War.

Thomas lived with his father in the Netherlands where he married the Dutch heiress Margaret van Hesse on 3 August 1659.

Charles II was forced to dismiss him, appointing in his stead Francis Howard, Baron of Effingham.

During this tumultuous time, Colepeper's erratic behaviour meant that he had to rely increasingly on his cousin and Virginia agent, Col. Nicholas Spencer.

Catherine Colepeper, his only child with his wife Margaret van Hesse, instead inherited much of his wealth and married Thomas Fairfax, lord of Cameron, in 1690.