In 1985 Schaffer founded the power/thrash metal band [a=Purgatory (11)], which changed its name to Iced Earth in 1988.
He is the only remaining original member of Iced Earth since 1991. Schaffer has also recorded and toured with Demons & Wizards, his side project with Blind Guardian vocalist Hansi Kürsch. He is also brother-in-law of former Iced Earth singer Matthew Barlow, as Matt is married to Jon's sister Kate Barlow.
In January of 2021 Schaffer was arrested by the FBI for his part in the US Capitol insurrection.