In July 1577 he and other students of law formed a community in the town of Douay and resided together in a rented house.
Ely was hooted as a traitor in the streets of Douay, and the members of his community and of the English college were subjected to frequent domiciliary visits; which satisfied the municipal authorities but not the populace.
The mayor, supposing that Ely was a military man, requested him to convey Cottam to London and hand him over to Lord Cobham, governor of the Cinque ports.
On 22 July 1586 he left Rheims for Pont-à-Mousson, where he had been appointed by the Duke of Lorraine to the professorship of the canon and civil laws, and he occupied that chair till his death on 15 March 1603–4.
This work, elicited by Robert Parsons's 'Brief Apology,’ was written by Ely shortly before his death and published by an anonymous editor, probably Dr. Christopher Bagshaw.
Ely wrote in English, with a view to publication, the lives of some of the martyrs in Elizabeth's reign, as appears from a letter addressed by him from Pont-à-Mousson, 20 June or July 1587, to Father John Gibbons, S. J., rector of the college of Treves.