[1] On 17 July 1765 Nelis was appointed a prebendary of Tournai Cathedral, resigning as university librarian on 26 November 1768 after numerous complaints that he was no longer fulfilling his obligations.

[2] He was nominated as bishop of Antwerp on 15 February 1785, his appointment was confirmed by Pope Pius VI on 25 April, and he was consecrated on 5 June.

Although initially a supporter of Emperor Joseph II's reform programme, he gradually came under suspicion of inspiring resistance to radical change, and on 26 October 1788 his arrest was ordered and he went into hiding.

After the collapse of the union in December 1790, he eventually came to support the claim of Francis II, Holy Roman Emperor, to rule in the Low Countries.

[1] During the French Revolutionary War in the Low Countries Nelis sought refuge first in the Netherlands and then in Germany, eventually making his way to Italy in 1795.