He came to prominence through his collaboration with the great Malayalam director Padmarajan. This productive collaboration saw the detailed screenplay and cinematography of Padmarajan become a fertile ground for expressive musical narration and thematic scores for Johnson. This is seen in some of the greatest motion pictures of Malayalam cinema, like Namukku Parkkan Munthiri Thoppukal (1986), Oru minnaaminungintaey nurunguvettam (1987), Nombarathipoovu (1987) and Perumthachan (1990). He is also noted for his collaboration with the Malayalam lyricist Kaithapram Damodaran Namboothiri. Johnson is affectionately called as the 'John Williams' of Malayalam cinema, after the legendary Hollywood composer John Williams. Johnson won the Indian National award as Best Film Composer for two consecutive years. He won his first National Award in (1993) for the motion picture Ponthan Mada. The next year he got his second award for the film Sukrutham (1994). His skilful integration of textual rhythm of the lyrics together with rich tonal arrangement, redefined songwriting in Malayalam cinema, since the late 1980s. In his film scores, Johnson combines native South Indian melodic patterns with the harmonic structure of European classical music and this has attained an expressive form of narration through film score