Midhun began his film career through Arvind Sastry's directorial Kahi released in 2016. The film took one and a half year to release and Midhun's score was generally appreciated after release.[3] Reviewer from The News Minute wrote "The genre-bending soundtrack composed by Midhun Mukundan, in particular, marks itself off as one of the stars of the show, setting and unsettling moods with equal rapidity".[4] Even before the release of Kahi, Midhun met filmmaker and actor Raj B. Shetty who was looking out for a newcomer for his film Ondu Motteya Kathe (2017).[5] The music was widely recognized and appreciated upon release. His other works in 2017 include Srinivasa Kalyana followed by a single track score for the film Kaafi Thota. The soundtrack of "Ondu Motteya Kathe" was well received and marked the beginning of Midhun's association with director-actor Raj[6]
Midhun's biggest breakthrough came with Raj B. Shetty and Rishab Shetty starrer gangster film Garuda Gamana Vrishabha Vahana (GGVV)(2021). The soundtrack won him Best Music Director nomination at the SIIMA Awards.[8] Midhun went on to say that working for this film was his most creatively satisfying project in his career.[9] Impressed by his work in the film GGVV, Malayalam director Nissam Basheer signed him for his psychological thriller film Rorschach (2022) starring Mammootty in the lead role.[10] This marked the Malayalam film score debut of Midhun.[11] In the same year, Midhun worked on some Kannada films such as Sakutumba Sametha, Dasara and Ramanu Kaadige Hodanu.
In 2023, Midhun collaborated with Raj B. Shetty the third time with the film Toby. His other releases include Poovan and Ramachandra Boss & Co both in Malayalam and Swathi Mutthina Male Haniye in Kannada. He debuted in Telugu cinema by composing a single song for the film Kota Bommali PS.[12]