Goodman became one of the Court preachers and was chaplain to [[Anne of Denmark|Queen Anne]], wife of [[James I of England|James I]]. His leaning towards [[Roman Catholicism]] made enemies for him at Windsor, and he was reprimanded by the King over Court sermons. A few years later, he was severely reprimanded for having erected a crucifix at Windsor and using altar-cloths with a cross design in his own cathedral at Gloucester, and further for having suspended a minister who insisted on preaching "that all who die papists go inevitably to hell".
It is likely that doubts were arising in his mind about the legitimacy of the Church's separation from [[Roman Catholic church|Rome]], and he sought the society of Catholic priests who were in hiding throughout the country
In 1643, Goodman's episcopal palace was pillaged by parliamentarian soldiers and over the course of a couple of years he was stripped of all his emoluments. He withdrew from public life to his small Welsh estate in [[Carnarvon]], and it is likely that he converted to Catholicism at this time.