In 1642 Marshall was appointed lecturer at St Margaret's, Westminster, and delivered a series of addresses to the Commons in which he advocated episcopal and liturgical reform.
He had a share in writing Smectymnuus, was appointed chaplain to the Earl of Essex's regiment in 1642, and a member of the Westminster Assembly in 1643.
He represented the English Parliament in Scotland in 1643, and attended the parliamentary commissions at the Uxbridge Conference in 1645.
He was with Archbishop Laud before the latter's execution, and was chaplain to King Charles I at Holmby House and at Carisbrooke Castle.
He died in November 1655 and was buried in Westminster Abbey, but his body was exhumed and maltreated at the Restoration.