He remained Kantor at the Thomaskirche until his death in 1750, composing three complete annual cycles of church cantatas, other sacred works—including a Magnificat, the St. Matthew Passion, and the Mass in В Minor—numerous secular cantatas, and a large amount of keyboard and instrumental music. The cantata cycles and the other great sacred works of his Leipzig years may well have been, as scholar Christoph Wolff has suggested, the means by which Bach sought to forge "an argument for the existence of God." During his final decade he completed the score of the Mass in В Minor, wrote the Goldberg Variations, and undertook two remarkable series of contrapuntal studies that summarized his knowledge of the art and theory of music: A Musical Offering and The Art of Fugue. With these speculative, large-scale, elaborately contrapuntal works he fittingly capped his own career and sounded the last, exquisite cry of the Baroque.

Bach was the consummate student and practitioner of musical science in the 18th century, much as Sir Isaac Newton, a generation and a half older than he, had been the consummate investigator of physical science. Both, by virtue of their innate genius and systematic approach to the phenomena that interested them, brought about revolutions in their fields of study. Newton's work became the foundation of modern science and Bach's the prototype for the organically conceived, highly structured "pure music" of the 19th and 20th centuries.The full panoply of musical style known to the late Baroque, from the rigorous imitative polyphony of the Renaissance to the breezy directness of Italian opera buffa, is recapped in Bach's works. His cantatas and large-scale sacred works make use of text-setting techniques absorbed from the Franco-Flemish composers of the 16th century, from 17th-century Italian sacred music, and from opera. His organ works respond to Italian and north-German influences, while hismusic for harpsichord is a brilliant amalgam of French and German elements. Bach's concertos have the grace and fluency of the finest Italian essays, with more contrapuntal density and melodic interest. His orchestral suites pay homage to the grandeur of the French style while surpassing the efforts of others (save Handel perhaps) in vitality; in the Suite No. 2 in В minor, BWV 1067, he even tips his hat in the concluding "Badinerie" to the emerging  galant. 

Bach cultivated virtuosity on a consistent basis, which has given his instrumental works an exceptional influence on works written subsequently, along with an enduring place in the repertoire. The sonatas and partitas for unaccompanied violin, the suites for unaccompanied cello, the sonatas for flute and harpsichord, the solo organ works, and the solo keyboard works including Das Wohltemperirte Clavier {The Well-Tempered Clavier) and Goldberg Variations are the foundation of the solo repertoire for these instruments. While the revival of interest in early music has brought the compositions of many of his predecessors back into circulation, the standard repertoire—instrumental, orchestral, and sacred—truly begins with Bach.

Nevertheless, for many years after his death the immensity of Bach's achievement as a composer remained hidden from posterity, even from the most knowledgeable and astute of his successors. Surprisingly little of his music was published during his lifetime, and the great works for which he is revered today existed only in manuscript or fair copies at the time of his death. Insiders like Mozart and Beethoven, who encountered Bach's music via these sources (or through contact with his students and sons), may have had an inkling of his greatness, but the public at large would begin to "discover" Bach only after a revival of interest in his music got under way early in the 19th century.