During the last two decades of his life, Josquin's fame spread abroad along with his music. The newly developed Technology of printing made wide dissemination of his music possible, and Josquin was the favorite of the first printers: one of Petrucci's first publications, and the earliest surviving print of music by a single Composer, was a book of Josquin's masses which he printed in Venice in 1502. This publication was successful enough that Petrucci published two further volumes of Josquin's masses, in 1504 and 1514, and reissued them several times.

In writing polyphonic settings of psalms, Josquin was a pioneer, and psalm settings form a large proportion of the motets of his later years. Few composers prior to Josquin had written polyphonic psalm settings. Some of Josquin's settings include the famous Miserere, written in Ferrara in 1503 or 1504 and most likely inspired by the recent execution of the reformist monk Girolamo Savonarola, Memor esto verbi tui, based on Psalm 119, and two settings of De profundis (Psalm 130), both of which are often considered to be among his most significant accomplishments.

Josquin went directly from Ferrara to his home region of Condé-sur-l'Escaut, southeast of Lille on the present-day border between Belgium and France, becoming provost of the collegiate church of Notre-Dame on 3 May 1504, a large musical establishment that he headed for the rest of his life. While the chapter at Bourges Cathedral asked him to become master of the choirboys there in 1508, it is not known how he responded, and there is no record of his having been employed there; most scholars presume he remained in Condé. In 1509, he held concurrently provost and choir master offices at Saint Quentin collegiate church.

The difficulties in compiling a works list for Josquin cannot be overstated. Because of his immense prestige in the early sixteenth century, many scribes and publishers did not resist the temptation of attributing anonymous or otherwise spurious works to Josquin. The German Editor Georg Forster summed up the situation admirably in 1540 when he wrote, "I remember a certain eminent man saying that, now that Josquin is dead, he is putting out more works than when he was alive." Thus, the authenticity of many of the works listed below is disputed on stylistic grounds or problems with sources or both. This thorny issue has been taken up vigorously in the now nearly complete New Josquin Edition (NJE).

Josquin's fame lasted throughout the 16th century, and indeed increased for several decades after his death. Zarlino, writing in the 1580s, was still using examples from Josquin in his treatises on composition; and Josquin's fame was only eclipsed after the beginning of the Baroque era, with the decline of the pre-tonal polyphonic style. During the 18th and 19th centuries Josquin's fame was overshadowed by later Roman School Composer Palestrina, whose music was seen as the summit of polyphonic refinement, and codified into a system of composition by theorists such as Johann Fux; however, during the 20th century, Josquin's reputation has grown steadily, to the point where scholars again consider him "the greatest and most successful Composer of the age." According to Richard Sherr, writing in the introduction to the Josquin Companion, addressing specifically the shrinking of Josquin's canon due to correction of misattributions, "Josquin will survive because his best music really is as magnificent as everybody has always said it was."

According to an account by Claude Hémeré, a friend and librarian of Cardinal Richelieu whose evidence dates as late as 1633, and who used the records of the collegiate church of Saint-Quentin, Josquin became a choirboy with his friend and colleague the Franco Flemish Composer Jean Mouton at Saint-Quentin's royal church, probably around 1460. Doubt has been cast on the accuracy of Hémeré's account, however. Josquin may have studied counterpoint under Ockeghem, whom he greatly admired throughout his life: this is suggested both by the testimony of Gioseffo Zarlino and Lodovico Zacconi, writing later in the 16th century, and by Josquin's eloquent lament on the death of Ockeghem in 1497, Nymphes des bois/Requiem aeternam, based on the poem by Jean Molinet. All records from Saint-Quentin were destroyed in 1669; however the collegiate chapel there was a center of music-making for the entire area, and in addition was an important center of royal patronage. Both Jean Mouton and Loyset Compère were buried there and it is certainly possible that Josquin acquired his later connections with the French royal chapel through early experiences at Saint-Quentin.

Since the 1950s Josquin's reputation has been boosted by the increasing availability of recordings, of which there are many, and the rise of ensembles specializing in the performance of 16th century vocal music, many of which place Josquin's output at the heart of their repertoire.

In the domain of secular music, Josquin left numerous French chansons, for from three to six voices, as well as a handful of Italian secular songs known as frottole, as well as some pieces which were probably intended for instrumental performance. Problems of attribution are even more acute with the chansons than they are with other portions of his output: while about 70 three and four-voice chansons were published under his name during his lifetime, only six of the more than thirty five- and six-voice chansons attributed to him were circulated under his name during the same time. Many of the attributions added after his death are considered to be unreliable, and much work has been done in the last decades of the 20th century to correct attributions on stylistic grounds.

Josquin's earliest chansons were probably composed in northern Europe, under the influence of composers such as Ockeghem and Busnois. Unlike them, however, he never adhered strictly to the conventions of the formes fixes – the rigid and complex repetition patterns of the rondeau, virelai, and ballade – instead he often wrote his early chansons in strict imitation, a feature they shared with many of his sacred works. He was one of the first composers of chansons to make all voices equal parts of the texture; and many of his chansons contain points of imitation, in the manner of motets. However he did use melodic repetition, especially where the lines of text rhymed, and many of his chansons had a lighter texture, as well as a faster tempo, than his motets.

Josquin wrote both sacred and secular music, and in all of the significant vocal forms of the age, including masses, motets, chansons and frottole. During the 16th century, he was praised for both his supreme melodic gift and his use of ingenious technical devices. In modern times, scholars have attempted to ascertain the basic details of his biography, and have tried to define the key characteristics of his style to correct misattributions, a task that has proved difficult, as Josquin liked to solve compositional problems in different ways in successive compositions—sometimes he wrote in an austere style devoid of ornamentation, and at other times he wrote music requiring considerable virtuosity. Heinrich Glarean wrote in 1547 that Josquin was not only a "magnificent virtuoso" (the Latin can be translated also as "show-off") but capable of being a "mocker", using satire effectively. While the focus of scholarship in recent years has been to remove music from the "Josquin canon" (including some of his most famous pieces) and to reattribute it to his contemporaries, the remaining music represents some of the most famous and enduring of the Renaissance.

While in Milan, Josquin wrote several examples of a new type of piece developed by the composers there, the motet-chanson. These compositions were texturally very similar to 15th century chansons in the formes fixes mold, except that unlike those completely secular works, they contained a chant-derived Latin cantus-firmus in the lowest of the three voices. The other voices, in French, sang a secular text which had either a symbolic relationship to the sacred Latin text, or commented on it. Josquin's three known motet-chansons, Que vous madame/In pace, A la mort/Monstra te esse matrem, and Fortune destrange plummaige/Pauper sum ego, are similar stylistically to those by the other composers of the Milan chapel, such as Loyset Compère and Alexander Agricola.

In parody masses, the source material was not a single line, but an entire texture, often of a popular song. Several works by Josquin fall loosely into this category, including the Missa Fortuna desperata, based on the three-voice song Fortuna desperata (possibly by Antoine Busnois); the Missa Malheur me bat (based on a chanson variously ascribed to Obrecht, Ockeghem, or, most likely, Abertijne Malcourt); and the Missa Mater Patris, based on a three-voice motet by Antoine Brumel. The Missa Mater Patris is probably the first true parody mass to be composed, for it no longer contains any hint of a cantus firmus. Parody technique was to become the most usual means of mass composition for the remainder of the 16th century, although the mass gradually fell out of favor as the motet grew in esteem.