In the Civil War, he chose the Parliamentary side and became colonel of Horse in General Fairfax's regiment.
In the course of the war he besieged his father's mansion at Faringdon in Berkshire (now Oxfordshire), which the latter had allowed the Royalists to garrison.
In 1660 he presented a petition from the county of Berkshire, complaining of the lack of a settled form of government and as a result was committed to the Tower of London for a breach of privilege.
He moved for Habeas Corpus, but judge Richard Newdigate decided that the court of King's Bench did not have the power to discharge him.
[5] Pye inherited his father's ruinous estates in 1662 and eventually died in December 1701 and was buried in All Saints' Church, Faringdon.