Mendelssohn substantially altered the work in his famous 1829 performance in Berlin. He changed the orchestration and the harmonies, and cut quite a bit of it. Norrington told the Guardian, "It's hugely cut. There's less than half left. Huge numbers of the meditative arias and chorales have gone. The story line is there, but I suppose [Mendelssohn] thought people couldn't handle four hours, three and half hours, whatever it is."

Norrington also doubted that this version of the work should be performed outside of a Mendelssohn festival. "That's the one time to hear it," he said, "but even so I think you've got to explain to the audience what we're doing and that it's not some sort of affectation, and neither is it the Matthew Passion that we know and love."

Mendelssohn is often given credit for discovering the work, which was said not to have been performed in public since Bach's death in 1750, and reintroducing it to audiences, igniting a "Bach revival." His 1829 performance of the piece: given when Mendelssohn was a 20-year-old prodigy: was widely attended, not just by ordinary music lovers but by the King of Prussia, Nicolo Paganini, and Friedrich Hegel.

Although Berlin's Kapellmeister Gaspare Spontini tried to block further performances, the work was performed twice more in 1829, once conducted by Mendelssohn, and once by his teacher Carl Friedrich Zelter.

In 1841, Mendelssohn revived the St. Matthew Passion in Leipzig: in Bach's own church, the Thomaskirche: and restored some of what was cut from the 1829 performance.