During the 1690s, he translated a number of books into German from Italian and French, completed and published his best-known novel, the satirical Der musicalische Quack-Salber (1700), and devoted his spare time to studying various subjects such as mathematics, Hebrew and Greek.

"[2] Not only health troubles, but also efforts by rival musicians and composers such as Georg Philipp Telemann and Kuhnau's own student Johann Friedrich Fasch, undermined his activities as Kantor.

It contains six sonatas, each outlining a biblical story in several contrasting movements: Kuhnau uses a wide variety of musical devices to portray the series of events (the sounding of trumpets, the hurling of David's stone, etc.)

These devices are not limited to changes of texture or harmony, but also include quotations from Protestant chorales (the Israelites' prayer is based on Luther's Aus tiefer Not schrei ich zu dir) and imitations of operatic arias (Gideon's fear).

Later research has shown that it was rather the first keyboard sonata published in Germany and that Kuhnau simply followed the naming convention established by contemporary foreign composers.

Unlike those of his predecessors at the Thomaskirche, Kuhnau's cantatas feature a unified approach to form: most begin with an instrumental section followed by alteration of arias and recitatives.

[1] The Christmas cantata Uns ist ein Kind geboren, formerly attributed to Bach as BWV 142, was most likely composed by Kuhnau.

[10] Of the few surviving books and treatises by Kuhnau, perhaps the most important is Der musicalische Quack-Salber ("The Musical Quack"), a satirical novel published in 1700.

It describes the fictional exploits of Caraffa, a German charlatan who strives to make a name for himself as musician by posing as an Italian virtuoso.

The novel's literary qualities have been noted, one writer venturing to call it linguistically innovative,[11] and it has also proven to be a singularly valuable source for performance practices of the late 17th century.

[14] Kuhnau's theoretical treatise Fundamenta compositionis survives in a single manuscript which also contains an anonymous treatise on double counterpoint (Kurtze doch deutliche Reguln von den doppelten Contrapuncten) and two texts by Christoph Bernhard; the entire manuscript was at one point attributed to Johann Sebastian Bach.

The similarity raised an important question about Walther's well-known and highly regarded treatise: how heavily was it based upon Kuhnau's lost original?

His views on musical modes, solmization, and other matters are preserved in a letter dated 8 December 1717, published by Mattheson in Critica musica in 1725.

[1] In addition, the "Biblical Sonatas" include a large preface in which Kuhnau explores the idea of program music and various related matters.