Born in Berlin, Marcus Merkel studied conducting, composition, piano and singing in Berlin. In his youth he was also trained as a jazz pianist and singer, as well as on the double bass and saxophone. Among other things, he won the German National Composition Competition four times and most recently the competition for the Festival Fanfare of the Graz University of Technology. He attended courses with Gianluigi Gelmetti, among others, and was a guest student of Christian Thielemann in Bayreuth. Marcus Merkel founded the Junge Philharmonie Berlin while still a student and is its artistic director. During this time, he also conducted a festival in Kyoto, Japan, led a conducting workshop for the Berlin Philharmonic's education department, and filled in for Julien Salemkour in a production of "Le Nozze di Figaro" in Rostock.

From the 2015/16 season he was engaged first as a solo repetiteur with conducting duties, later as Kapellmeister at the Graz Opera, where he conducted over 40 performances per season, including pieces such as Die Königskinder, Norma, Don Carlo, La Forza del Destino and Der fliegende Holländer. Marcus Merkel conducted rehearsals of premieres such as Die Fledermaus, Candide, Le Nozze di Figaro and Les pêcheurs de perles.Highlights during his time in Graz included an Ariadne auf Naxos in Amsterdam, the rehearsal of all Beethoven piano concertos for Rudolf Buchbinder, a Verdi Requiem in the Berlin Cathedral, a concertante Fidelio with Sir Bryn Terfel and a semi-staged Tosca with Kristine Opolais, Jonas Kaufmann and Ludovic Tézier. Furthermore, Merkel founded the Junge Konzerte Graz, with which he regularly organizes concerts by young musicians for young people. To expand his leadership skills, he completed an MBA degree on the side.

Since the 2022/23 season, Marcus Merkel has been chief conductor at Theater Koblenz and has previously made guest appearances with a premiere production of Parsifal. In his first year as chief conductor, he made his debut with the Antwerp Symphony Orchestra and rehearsed the premieres of Freischütz, La Traviata and Nixon in China in Koblenz. In the summer of 2023 he celebrated a great success in Graz with a Carmen with Elina Garanča, Ramón Vargas and Erwin Schrott. In the 2023/24 season he is premiering La clemenza di Tito, Hänsel und Gretel and Ariadne auf Naxos in Koblenz. Guest engagements take him to the Staatstheater Darmstadt for a symphony concert, to the Berliner Dom for a Verdi Requiem and to Graz for a concert version of the Ring des Nibelungen with Klaus Florian Vogt and Michael Volle. In 2024/25 he returns to Antwerp for a symphony concert and makes his debut at the Semperoper Dresden with a performance series of Die Fledermaus.