His primary organ works are the Three Preludes and Fugues, Op. 37 (1837), and the Six Sonatas, Op. 65 (1845), of which Eric Werner wrote "next to Bach's works, Mendelssohn's Organ Sonatas belong to the required repertory of all organists".
Hans vigtigste orgelværker er Tre Præludier og Fugaer, opus 37 (1837), og de Seks Sonater, opus 65 (1845), om hvilke Eric Werner skrev: ”Sammen med Bachs værker er Mendelssohns orgelsonater obligatoriske for enhver organist.”