[3] The congregation at Geneva chose John Knox and Goodman in September 1555 for their pastors, and the two formed a lifelong friendship.
During his exile Goodman took part in Miles Coverdale's translation of the Bible and helped Knox in the "book of common order".
The most famous by Goodman was entitled How superior Powers ought to be obeyed of their subjects, and wherein they may lawfully be by God's word disobeyed and resisted .
The book, in favor of Wyatt's rebellion, bitterly attacked Mary I of England and the government of women in general, which afterwards drew down Elizabeth's displeasure upon the author.
Goodman also published while abroad a Commentary upon Amos, in which he likens Mary to Proserpine, queen of Hades.
In October he was made one of the council appointed by the lords of the congregation to treat of religion, he and Knox preaching daily.
[3] Intercessions were meanwhile made for his return to England, though John Calvin exhorted him to finish his work in Scotland.
He went to Ireland (January 1566) as chaplain to Sir Henry Sidney, the new lord deputy, who in the spring of 1567 recommended him to be bishop of Dublin and promised him the deanery of St. Patrick's Cathedral.
[6] He was obliged to make a full recantation of his published opinions, and a protest in writing of his dutiful obedience to the queen's person and her lawful government.
[3] In 1584 Goodman refused to subscribe to the articles and the service book, and Archbishop John Whitgift complained of his perversity to the lord treasurer.
When James Ussher came to England to collect books for the Dublin Library, he visited Goodman (4 June 1603), then lying on his deathbed.