At the end of World War II the autograph of Così fan tutte was split up. Act I disappeared for several decades and re-emerged only in the 1970s. It is now kept in the Biblioteka Jagiellońska in Kraków. Act II is in the Musikabteilung of the Staatsbibliothek zu Berlin, Preußischer Kulturbesitz. One bifolium containing ‘Tutti accusan le donne’ became separated from the main part of the autograph apparently at quite an early date, since it appears never to have been bound. It was discovered by Plath in the Frankfurt Stadt- und Universitatsbibliothek.Its bifoliation number, 18 (the correct number in the original sequence), suggests that it was once with the main autograph. Missing from the autograph of Act II and not so far located is the chorus ‘Secondate’ and the accompagnato ‘Ei parte’. Two linked recitatives (‘Come tutto congiura’ / ‘L’abito di Ferrando’) are now bound in with the autograph on two unnumbered bifolia, but they are in a copyist's hand. Mozart's originals apparently do not survive. Another significant element that exists only in a copyist's hand is the five-bar repeat of the ‘magnetic’ music for wind instruments in the Act I finale. This appears on a separate leaf, albeit in conjunction with a continuity indication from Mozart in the main score. Finally, the wind parts that Mozart copied on separate leaves in the larger ensembles are no longer extant in his hand.

There are two fragments of versions of ‘Donne mie’: the first resembles very closely the opening of the final version; the second is quite different, apparently combining some words from the text of ‘Donne mie’ with a musical figure used in Guglielmo's discarded Act I aria ‘Rivolgete’. A replacement for the canon quartet in the Act II finale in Mozart's hand is also extant. There are only two sketches. Various drafts for the canon quartet itself appear on a leaf in the Internationale Stiftung Mozarteum in Salzburg. A photograph of a further leaf containing some brief sketches for bars 545–74 of the Act II finale is in the Osterreichische Nationalbibliothek in Vienna.