The plot of The Saragossa Manuscript is punctuated, or counterpointed, with eerie sounds by one of the makers of contemporary musical avant-garde, Polish composer Krzysztof Penderecki. While the various doiiings and ploiiings can readily be associated with his style of the time, Penderecki has astonished the critics with the ease with which he moves around a more 'Classical' sound. Three of his short compositions written for the film, Aria and two Minuets, have been published much later as Three Pieces in Antique Style; they are now considered a very early prediction of his later return to tradition evident in such masterpieces as Credo or The Seven Gates of Jerusalem.

Yet it is the introductory piece that is probably of the greatest significance for the movie's general message. In the words of Polish writer Ewa Siemdaj:

The music in The Saragossa Manuscript it is a stylistic pastiche of late Baroque and early Classicism, a blend of Vivaldi and of early Mozart. The 'overture' itself is a clear suggestion of that. The string passages seem a direct import from Vivaldi; the horn signal is nothing else than a pastiche of a Mozart divertimento. The oft-mentioned quotation from Beethoven's Ninth Symphony (to be procise, of its fourth movement) is, in fact, a quasi-quotation, for Penderecki has adapted the famous fragment of the first stanza of 'Ode to Joy' to be performed by a much smaller ensemble; the original would require solo counterbasses and, later, choir with orchestra.