As a child, Gibbons sang in the Chapel Royal under the direction of Giles. Gibbons most likely studied with his father. After his father's death in 1625, Gibbons moved to Exeter to live with his uncle.
In 1638, Gibbons succeeded organist Thomas Holmes and began playing in the Winchester Cathedral. The Civil War, however, lead to a suppression of Church music, and it put an end to his position. He later moved to London where he lived from 1651 to 1660. He worked with Matthew Locke on the masque Cupid and Death in 1653.