Born in Neuilly-Plaisance, Margoni studied harmony with Henri Challan, counterpoint and fugue with Noël Gallon, orchestral conducting with Louis Fourestier, musical analysis with Olivier Messiaen and Ondes Martenot with Maurice Martenot.
In the competition for the Prix de Rome in 1957 and 1958 he won a second prize each and in 1959 the Premier Grand Prix with the cantata Dans les Jardins d’Armide after Torquato Tasso's Jerusalem Delivered.
He then held a chair in musical analysis at the Conservatoire de Paris.
He also acted as a conferencier, conductor, improviser with the Ondes Martenot, pianist and music theorist and musical comedian, the latter with Jérôme Deschamps and Alain Germain.
For Germain he wrote the music for the play Un piano pour deux pianistes, in which he himself performed with Pascal Le Corre in 1987.