In 1579 Elizabeth began having talks about the possibility of marrying the Duke of Anjou from France. Stubbs wrote a pamphlet criticizing the proposed marriage. Stubbs objected to the fact that the Duke of Anjou was a Catholic. He also argued that, at forty-six, Elizabeth was too old to have children and so had no need to get married.
Elizabeth was furious and ordered that Stubbs and the publisher of the pamphlet should be arrested. At first Elizabeth wanted the men to be hanged, but eventually she decided that the men should have their right hands cut off.
John Stubbs, who was elected to the House of Commons in 1589, died in 1590.