[6] Starting in the late 16th century, a legend began that the second of these points, the threat that polyphony might have been banned by the Council because of the unintelligibility of the words, was the impetus behind Palestrina's composition of this mass.

It was believed that the simple, declamatory style of Missa Papae Marcelli convinced Cardinal Carlo Borromeo, on hearing, that polyphony could be intelligible, and that music such as Palestrina's was all too beautiful to ban from the Church.

In 1607, the composer Agostino Agazzari wrote: Music of the older kind is no longer in use, both because of the confusion and babel of the words, arising from the long and intricate imitations, and because it has no grace, for with all the voices singing, one hears neither period nor sense, these being interfered with and covered up by imitations...And on this account music would have come very near to being banished from the Holy Church by a sovereign pontiff [Pius IV], had not Giovanni Palestrina founded the remedy, showing that the fault and error lay, not with the music, but with the composers, and composing in confirmation of this the Mass entitled Missa Papae Marcelli.Jesuit musicians of the 17th century maintained this rumor, and it made its way into music history books into the 19th century, when historian Giuseppe Baini, in his 1828 biography of Palestrina, couched him as the "savior of polyphony" from a council wishing to wipe it out entirely: On Saturday, 28 April 1565, by order of Cardinal Vitellozzi, all the singers of the papal chapel were gathered together at his residence.

Their Eminences heaped their congratulations on the composer, recommending to him to go on writing in that style and to communicate it to his pupils.An entry in the papal chapel diaries confirms that a meeting such as the one described by Baini occurred, but no mention is made of whether the Missa Papae Marcelli was performed there or what the reaction of the audience was.

In the latter part of the 20th century, the Missa Papae Marcelli has been recorded frequently, and is often used as a model for the study of stile antico Renaissance polyphony in university courses on music.

Richard Taruskin described the Credo as "a strategically planned series of cadential 'cells' ... each expressed through a fragment of text declaimed homorhythmically by a portion of the choir ... and rounded off by a beautifully crafted cadence".

As was frequently done in the 16th century, Palestrina adds an extra voice in Agnus Dei II, making seven for this movement, in which is embedded a three-part canon that begins with the head-motive.