Vogler was born at Pleichach in Würzburg. His father Jared Vogler, a violin maker, while educating him in the Jesuit college, encouraged his musical talent, which was so marked that at ten years old he could not only play the organ well, but had also acquired a fair command of the violin and some other instruments. In 1771 he went to Mannheim, where he composed a ballet for the elector Karl Theodor, who sent him to Bologna in 1774 to study under the Padre Martini. Dissatisfied with the method of that learned theorist, he studied for five months under Francesco Antonio Vallotti at Padua, and afterwards proceeded to Rome, where, having been ordained priest, he was admitted to the famous Academy of Arcadia, made a knight of the Golden Spur, and appointed protonotary and chamberlain to the pope.
On his return to Mannheim in 1775, Vogler was appointed court chaplain and second maestro di cappella. He now established his first great music school. His pupils were devoted to him, but he made innumerable enemies, for the principles upon which he taught were opposed to those of all other teachers. He had invented a new system of fingering for the harpsichord, a new form of construction for the organ, and a new system of musical theory founded upon that of Valotti. Mozart condemned the fingering as "miserable," and many rumours to his discredit have survived to this day owing to Mozart's share in the prejudice felt against him. The proposed change in the construction of the organ consisted in simplifying the mechanism, introducing free-reeds in place of ordinary reed-stops, and substituting unisonous stops for the great "mixtures" then in vogue. The theoretical system, though professedly based upon Valotti's principles, was to a great extent empirical. Nevertheless, in virtue of a certain substratum of truth which seems to have underlain his new theories, Vogler undoubtedly exercised a powerful influence over the progress of musical science, and numbered among his disciples some of the greatest geniuses of the period.
In 1778 Karl Theodor moved his court to Munich. Vogler followed him there in 1780, but, dissatisfied with the reception accorded to his dramatic compositions, soon quit his post. He went to Paris, where after much hostility his new system was recognized as a continuation of that started by Rameau. His organ concerts in the church of St. Sulpice attracted considerable attention. At the request of the queen, he composed the opera Le Patriotism, which was produced before the court at Versailles. His travels were wide, and extended over Spain, Greece, Armenia, remote districts of Asia and Africa, and even Greenland, in search of uncorrupted forms of national melody. In 1786 he was appointed Kapellmeister by Gustav III of Sweden, founded his second music school in Stockholm, and attained extraordinary celebrity by his performances on an instrument called the "orchestrion", a species of organ invented by himself. In 1790 he brought this instrument to London, and performed upon it with great effect at the Pantheon, for the concert-room of which he also constructed an organ upon his own principles. The abbe's pedal-playing excited great attention. His most popular pieces were a fugue on themes from the Hallelujah Chorus, composed after a visit to the Handel festival at Westminster Abbey, and A Musical Picture for the Organ, by Knecht, containing the imitation of a storm.
From London Vogler proceeded to Rotterdam and the chief towns on the Rhine. At Esslingen he was presented with the "wine of honor", reserved for the use of sovereigns. At Frankfurt he attended the coronation of the emperor Leopold II. He then visited Stockholm, and after a long residence there, interrupted by endless wanderings, once more established himself in Germany, where his compositions, both sacred and dramatic, received at last full credit. We hear of him at Berlin in 1800, at Vienna in 1804 and at Münich in 1806. While at Frankfurt in 1807 he received an invitation from Ludwig I, grand duke of Hesse-Darmstadt, offering him the appointment of Kapellmeister, with the order of merit, the title of privy councillor, a salary of 3000 florins, a house, a table supplied from the duke's own kitchen, and other privileges, which determined him to bring his wanderings at last to a close.
At Darmstadt he opened his third and most famous music school, the chief ornaments of which were Gansbacher, Carl Maria von Weber and Giacomo Meyerbeer, whose affection for their old master was unbounded. One of Vogler's latest exploits was a journey to Frankfurt in 1810, to witness the production of Weber's Sylvana. He continued to work hard to the last, and died suddenly of apoplexy at Darmstadt. He was a brilliant and accomplished performer, and an excellent if an eccentric teacher; but his own compositions, save for a rarely heard requiem, have not survived.