The Pope appointed Allen to be a Canon in Courtray (now in West Flanders, Belgium, and known as Kortrijk), and he returned to Douai in July 1576, but there he had to face a new difficulty. Besides the plots to assassinate him by agents of the Queen of England, the rebels against the rule of the Spanish Crown, encouraged by Elizabeth and her emissaries, now present in Douai, expelled the students of the University from Douai in March 1578. Allen then re-established the College at Rheims, a city then under the patronage and protection of the House of Guise. The collegians took refuge at the University of Rheims, where they were well received, and continued their work as before, and Allen was soon afterwards elected a canon in the Chapter of Rheims Cathedral. Thomas Stapleton, Richard Bristow, Gregory Martin, and Morgan Phillips were amongst Allen's companions.