In recognition of its great devotion, and in deep gratitude for its valiant achievements, the Church and the nations of Europe continued to grant the Order numerous rights, privileges and prerogatives. These special immunities, unique grants and sacred rights were formally set forth in concordats with the Vatican, in several Papal Bulls, by the proclamations and recognition of some 90 popes, and in treaties with the Sovereigns of Europe.

Among the rights given and recognized by the papacy over several centuries were: The right of the Order to have its own churches, chapels, oratories, schools and cemeteries; to have its own convents, monasteries and seminaries; to choose and educate its own brothers and sisters; to select its own clerics and priests, who have been validly ordained, according to the Papal Bull of Anastasius IV; to remain free from interdiction and general excommunication; and to be exempt from the jurisdiction of all ordinaries, extraordinaries, cardinals and ecclesiastical courts.

It should be noted that at historic meetings at the Vatican, called and presided over by the Pope, at which the Prince Grand Master of the Order was in attendance, the Pope provided for the seating of the Prince Grand Master one elevation higher than the Cardinals, signifying his unique position of being above and independent of the hierarchy, and subject, in matters of religion, only to the Supreme Pontiff himself.

Over the centuries, numerous popes offered the cardinal's hat to the Grand Masters of the Order. Some accepted the honor. However, the later Grand Masters usually declined the recognition, because it was deemed to be a lower position than that which they held as head of the Order as history specifically records was done by two of the greatest Grand Masters of the Order L'Isle Adam and La Valette.