At nine years of age he entered the school for pages at the residence of Prince-Bishop Lamberg of Passau, who later proposed him for admittance to the Collegium Germanicum in Rome.

Owing to the friendship of Benedict XIV, Migazzi concluded several transactions to the satisfaction of the Habsburg Empress Maria Theresa, who in return appointed him in 1751 coadjutor to the aged Archbishop of Mechelen.

After twenty-five years of his administration, the Concilium locum tenens regium asked him if there was any priest in his diocese in possession of two benefices or offices, as in that case it was Emperor Joseph II's pleasure that one of them should be given up.

Maria Theresa and Kaunitz took a lively interest in his accounts of what transpired in the conclave (23 November 1775 – 16 February 1776), which elected Pope Pius VI who subsequently visited Vienna during the reign of Joseph II.

Joseph II, during his ten years' reign, published 6200 laws, court ordinances and decrees affecting the Catholic Church.

He mentioned thirteen "grievances" and pointed out for each the means of redress: laxity in monastic discipline; the general seminaries; marriage licenses; and the "Religious Commission", which assumed the position of judge of the bishops and their rights.

The Cardinal insisted on its abolition, stating: I am in all things your Majesty's obedient subject, but in spiritual matters the shepherd must say fearlessly that it is a scandal to all Catholics to see such fetters laid upon the bishops.

The scandal is even greater when such power is vested in worldly, questionable, even openly dangerous and disreputable men.In another matter, he wrote: The dismal outlook of the Church in your Majesty's dominion is all the more grievous from the fact that one must stand by in idleness, while he realizes how easily the increasing evils could be remedied, how easily your Majesty's conscience could be calmed, the honour of Almighty God, respect for the Faith and the Church of God be secured, the rightful activities of the priesthood set free, and religion and virtue restored to the Catholic people.

All this would follow at once, if only your Majesty, setting aside further indecision, would resolve generously and perseveringly to close once for all the sources of so great evil.The Emperor made concessions, greeted by Migazzi with satisfaction.