He was a committed Puritan, and he opposed the negotiations for marriage between Queen Elizabeth I and Francis, Duke of Anjou, a Roman Catholic who was the brother of the King of France.
In 1579 he put his opinions into a pamphlet entitled The Discovery of a Gaping Gulf whereunto England is like to be swallowed by another French Marriage, if the Lord forbid not the banns, by letting her Majesty see the sin and punishment thereof.
Stubbs undiplomatically described the proposed wedding as a "contrary coupling," "an immoral union, an uneven yoking of the clean ox to the unclean ass, a thing forbidden in the law" as laid down by St. Paul, a "more foul and more gross" union that would draw the wrath of God on England and leave the English "pressed down with the heavy loins of a worse people and beaten as with scorpions by a more vile nation."
Circulation of this pamphlet was prohibited, and Stubbs, his printer, and publisher William Page were tried at Westminster, found guilty of "seditious writing", and sentenced to have their right hands cut off by means of a cleaver driven through the wrist by a mallet.
At the time Stubbs protested his loyalty to the Crown, and immediately before the public dismemberment delivered a shocking pun: "Pray for me now my calamity is at hand.
Despite his punishment, he remained a loyal subject of Queen Elizabeth and later served in the House of Commons as MP for Great Yarmouth in the English Parliament of 1589.