When the First English Civil War began in 1642, he was a prominent leader of the Royalists in the West Country, and appointed Commissioner of Array for Somerset.

Although he was elected to the Cavalier Parliament in 1661, and appointed Knight Marshal in 1667, he failed to obtain what he considered adequate reimbursement for his losses in the civil war.

From 1629 to 1640, Charles ruled without Parliament, leading to a constant search for new sources of revenue; the most famous was ship money, others included the right to manufacture soap.

[5] Like Charles, Wyndham invested heavily in fenland reclamation, an undertaking that caused considerable local unrest, constant legal challenges, vast expense, and not completed until the 1650s.

He became a Colonel in the Royalist army, and recruited two regiments from the Somerset Trained Bands, the second commanded by his son, Sir Hugh.

[8] On 14 June 1645, the New Model Army under Sir Thomas Fairfax won a decisive victory over Prince Rupert at Naseby.

The New Model linked up with the Western Association Army under Edward Massey, and forced Lord Goring to retreat from Taunton.

His grandson Edmund became his heir; in 1690, his second wife, Elizabeth Savage, claimed she was near starvation due to his failure to pay her allowance.