Emanuel Bach was born in Weimar. When he was ten years old he entered the St. Thomas School at Leipzig, where his father had become cantor in 1723, and continued his education as a student of jurisprudence at the universities of Leipzig (1731) and of Frankfurt (Oder) (1735). In 1738, at the age of 24, he took his degree, but at once abandoned his prospects of a legal career and determined to devote himself to music.

A few months later (armed with a recommendation by Sylvius Leopold Weiss) he obtained an appointment in the service of Frederick II of Prussia ("Frederick the Great"), the then crown prince, and upon Frederick's accession in 1740 Emanuel became a member of the royal orchestra. He was by this time one of the foremost clavier players in Europe, and his compositions, which date from 1731, include about thirty sonatas and concert pieces for harpsichord and clavichord. During his time there, Berlin was a rich artistic environment, where Bach mixed with many accomplished musicians, including several notable former students of his father, and important literary figures, such as Gotthold Ephraim Lessing, with whom the composer would become close friends.

In Berlin he continued to write numerous musical pieces for solo keyboard, including a series of character pieces, the so called "Berlin Portraits," including La Caroline.

His reputation was established by the two published sets of sonatas which he dedicated respectively to Frederick the Great and to the grand duke of Württemberg. In 1746 he was promoted to the post of chamber musician, and served the king with the likes of Carl Heinrich Graun, Johann Joachim Quantz, and Franz Benda.

His publication, An Essay on the True Art of Playing Keyboard Instruments was a definitive work on technique. It broke with rigid tradition in allowing, even encouraging the use of the thumbs, and became the standard on finger technique for keyboards. The essay basically lays out the fingering for each chord and some chord sequences. The techniques are largely followed to this day. The first part of the Essay has a chapter explaining the various embellishments in work of the period, e.g., trills, turns, mordents, etc. The second part presents Emanuel Bach's ideas on the art of figured bass and counterpoint, where he gives preference to the contrapuntal approach to harmonization over the newer ideas of Rameau's theory of harmony and root progressions. Emanuel Bach's work was influential on, among others, Haydn, Mozart, and Beethoven.

During his residence in Berlin, he wrote a fine setting of the Magnificat (1749), in which he shows more traces than usual of his father's influence; an Easter cantata (1756); several symphonies and concerted works; at least three volumes of songs; and a few secular cantatas and other occasional pieces. But his main work was concentrated on the clavier, for which he composed, at this time, nearly two hundred sonatas and other solos, including the set Mit veränderten Reprisen (1760 – 1768) and a few of those für Kenner und Liebhaber. Meanwhile he placed himself in the forefront of European critics by his Versuch über die wahre Art das Clavier zu spielen, a systematic and masterly treatise which by 1780 had reached its third edition, and which laid the foundation for the methods of Muzio Clementi and Johann Baptist Cramer.

In 1768 Emanuel Bach succeeded Georg Philipp Telemann (his godfather) as director of music at Hamburg, and in consequence of his new office began to turn his attention more towards church music. The next year he produced his oratorio Die Israeliten in der Wüste (The Israelites in the Desert), a composition remarkable not only for its great beauty but for the resemblance of its plan to that of Felix Mendelssohn's Elijah, and between 1768 and 1788 wrote twenty - one settings of the Passion, and some seventy cantatas, litanies, motets, and other liturgical pieces. At the same time, his genius for instrumental composition was further stimulated by the career of Joseph Haydn.

He married Johanna Maria Dannemann in 1744. Only three of their children lived to adulthood – Johann Adam (1745 – 89), Anna Carolina Philippina (1747 – 1804) and Johann Sebastian (1748 – 78). None became musicians. Emanuel Bach died in Hamburg on 14 December 1788. He was buried in the Michaeliskirche (Church of St. Michael) in Hamburg.

Through the latter half of the 18th century, the reputation of Emanuel Bach stood very high. Wolfgang Amadeus Mozart said of him, "He is the father, we are the children." The best part of Joseph Haydn's training was derived from a study of his work. Ludwig van Beethoven expressed for his genius the most cordial admiration and regard. This position he owes mainly to his keyboard sonatas, which mark an important epoch in the history of musical form. Lucid in style, delicate and tender in expression, they are even more notable for the freedom and variety of their structural design; they break away altogether from both the Italian and the Viennese schools, moving instead toward the cyclical and improvisatory forms that would become common several generations later.

The content of his work is full of invention and, most importantly, extreme unpredictability, and wide emotional range even within a single work, a style that may be categorised as Empfindsamer Stil. It is no less sincere in thought than polished and felicitous in phrase. He was probably the first composer of eminence who made free use of harmonic colour for its own sake since the time of Lassus, Monteverdi, and Gesualdo. In this way, he compares well with the most important representatives of the First Viennese School. In fact he exerted enormous influence on the North German School of composers, in particular Georg Anton Benda, Bernhard Joachim Hagen, Ernst Wilhelm Wolf, Johann Gottfried Müthel, Friedrich Wilhelm Rust and many others. His influence was not limited to his contemporaries, and extended to Felix Mendelssohn and Carl Maria von Weber.

His name fell into neglect during the 19th century, with Robert Schumann notoriously opining that "as a creative musician he remained very far behind his father"; in contrast, Johannes Brahms held him in high regard and edited some of his music. The revival of Emanuel Bach's works has been underway since Helmuth Koch's rediscovery and recording of his symphonies in the 1960s, and Hugo Ruf's recordings of his keyboard sonatas. There is an ongoing effort to record his complete works, led by Miklos Spanyi on the Swedish record label BIS.