After completing a Master's degree in Scenography at The Royal Academy of Fine Arts in Ghent and a Master's degree in Costume Design at the Royal Academy of Fine Arts in Antwerp, he began his career at the Arena Theatre Ghent. He soon became resident costume designer and supervisor at the City Theatre in Ghent: NTG (now NT Ghent), where he collaborated with several distinguished directors, including Hugo Claus, Jean-Pierre Dedecker, Dirk Tanghe, Eddy Vereycken, Hugo van den Berghe, Guy Cassiers, and Victor Löw. In his final year at NTG, director Frank van Laecke invited him to design the costumes for the opera productions Cavalleria Rusticana and Pagliacci at the Italian Opera in Amsterdam. This marked the beginning of an intense and enduring collaboration. Since 1997, Marnik Baert has worked as an independent freelance designer on a wide range of national and international productions. In 1999, he was appointed Artistic Coordinator of the Costume Design Department at the Royal Academy of Fine Arts in Antwerp. He subsequently served as Professor of Costume Design at the Academy for twenty-three years. For Music Hall Group, he designed the international arena opera productions of La Bohème, Carmen, Nabucco, Aida, and La Traviata, all under the direction of Franck Van Laecke. Marnik Baert also created the stage and costume designs for numerous musical productions, including Peter Pan, Aladdin, Camelot, Oliver Twist, A Christmas Carol, and Oliver!. For Festivaria, he designed the sets for the musical Kiss Me Kate, and he served as co-director of The Wizard of Oz. He later designed the sets for Singin’ in the Rain and The Hunchback of Notre Dame. In 2006, he was invited by the Flemish Opera to create the set for Nino Rota’s opera Aladdin. The following year, he was responsible for both set and costume design for Les Mamelles de Tirésias by Francis Poulenc at the Grand Théâtre de Luxembourg. 

In 2021 and 2022, he designed sets for the prestigious Historalia musical productions Albert I, Rubens, and 1830. The following year, he created the set design for Marie Antoinette, an open-air production in Torhout, as well as for Historalia Productions. For Zomeropera Alden Biesen, he designed the sets for Don Pasquale, La Traviata, Die Fledermaus, Tosca, Il Trovatore, L'Italiana in Algeri, Rigoletto, Eugene Onegin, and Gianni Schicchi. Among his recent productions are set design for the Spectacle Musical 14-18 for Studio100, and both set and costume design for Hamlet, an Eén Zee production.