After the final entry of the fugal melody, the composition resolves to the key's corresponding major, B-flat, that is held. From there, a coda is played as a cadenza much like the Toccata itself, resolving to a series of chords followed by arpeggios that progress to other paired chords, each a little lower than the one preceding, leading to the signature finale that is as recognizable as the Toccata's introduction.
Buxtehude's organ works, like those of his contemporaries, are characterized by the presence of the stylus phantasticus, a performance style derived from improvisation. The stylus phantasticus included elements of excitement and bravura, with adventurous harmonies and sudden changes in registration. Buxtehude's free organ works made great use of these elements. These works generally began with a free section, followed by an imitative section (sometimes a full-blown fugue), then another free section, and then another imitative section (usually based on motivic material from the first imitative section), and finally another free section. BWV 565 derives several of its stylistic elements from this earlier form of organ music, in particular the stylus phantasticus.
In the Fugue, the F major episode (an elaboration of the Fugue subject) is nearly identical to a passage in a Fantasia in D minor by Johann Pachelbel. The original passage by Pachelbel is the source for Subject of Bach's Fugue, and its use is possibly a homage to the older composer. As noted in J. S. Bach's obituary, it was common practice for Bach to use other composers' work as inspiration for his own. (The Passacaglia and Fugue in C minor BWV 582 first half of the Basso Ostinato are taken form Andre Raison's G minor Passacaglia for Organ, The F Major 2 part invention's theme is derived from a G minor Concerto theme by Vivaldi, and numerous Organ Fugues were written on a number of Italian Composers themes; the term "Bach the Borrower" was coined as a result).
The exceptional number of fermatas and broken chords in the Toccata and Fugue BWV 565 has been explained by some (for example, Klaus Eidam; see references below) on the supposition that Bach composed it as a work to test an organ, which he did regularly. The first thing Bach is said to have done when testing an organ is to pull out all the stops and play in the fullest possible texture, in order to see if the organ had good bellows to provide plenty of wind to the instrument: not enough, and the pitch would be unsteady, and tone quality would be inferior. The opening of BWV 565, with its three opening flourishes and massive rolled chord, would serve as a good test for an organ's winding system.
On the other hand, renowned Bach scholar Christoph Wolff and others argue that the work is indeed by Bach, and is probably a transcription of an organ improvisation of the sort he used when testing organs, perhaps originating very early in his career, from the 1700s. Helmut Walcha, a respected 20th-century authority on Bach's organ works, also regarded the Toccata and Fugue as the original work of J.S. Bach. Even though Walcha was known to only include pieces that were undoubtedly authentic in his Bach organ recordings, the Toccata and Fugue in D minor appears in both of his complete recordings of Bach's organ works.
It is very unlikely that Ringk would have had knowledge of the work by Pachelbel alluded to in the F major episode. There is no proof that J Ringk was a pupil of Bach as Peter Williams contends. Very few of Bach's organ works survive in autograph score and many were discarded after they had been stylistically or structurally superseded as Bach's composition style matured. J. S. Bach did occasionally write consecutive fifths: for example, in the Fifth Brandenburg Concerto (which he later corrected to hidden octaves). Bach uses imperfect consecutive (similar motion) fifths, (diminished Fifth to Perfect Fifths) in his vocal works. These imperfect similar fifths are not avoided by Bach unless they appear between the soprano and bass.
The allegation that "various musical passages in the work are simply too crude musically to have been Bach's work" must be tempered by the likelihood that the piece is partly, even mostly, improvisational.
Williams also argues that the Toccata and Fugue was transcribed by Bach from an earlier work for violin.
Williams put his theory into practice by writing a reconstruction of the conjectured original violin work, which has been performed (by violinists Jaap Schröder and Simon Standage) and published. The violinist Andrew Manze subsequently produced his own reconstruction, also in A minor, which he has performed widely and recorded.
Bach is known to have transcribed solo violin works for organ at least twice. The Prelude first movement of the Partita in E major for solo violin, BWV 1006, was converted by Bach into the solo organ part of the opening movement of the Cantata BWV 29 Wir danken dir, Gott, wir danken dir. Bach also transcribed the Fugue movement of his Sonata in G minor for solo violin BWV 1001 as the second half of the Prelude and Fugue in D minor for organ, BWV 539.
The Disney film Fantasia, released in 1940, opens with Leopold Stokowski's transcription for large orchestra of the Toccata and Fugue. In 1927, the date of this transcription, authentic performance practice was still more than half a century away. Stokowski's first 78rpm disc of 1927 was an international best-seller which introduced the music to many record collectors. He recorded it several more times in subsequent years. Others who have transcribed the Toccata and Fugue for orchestra include Lucien Cailliet, Rene Leibowitz, Leonidas Leonardi, Alois Melichar, Eugene Ormandy, Fabien Sevitzky, Stanislaw Skrowaczewski, and Sir Henry Wood.
The work has been transcribed for wind ensemble several times, most notably by Erik Leidzen, Mark Hindsley, and Merlin Patterson.