The present invention relates to a method of controlling an indirect-injection engine, notably a supercharged engine, in particular a spark-ignition engine, comprising at least one cylinder (10) including a combustion chamber (12), at least two air intake means (14, 16) comprising each a pipe (18, 20) controlled by an intake valve (22, 24), at least one fuel injection means (26, 28) associated with each intake means and at least one burnt gas exhaust means (30) with an exhaust valve (32), said engine running according to two intake modes, a mode with burnt gas scavenging and a mode without scavenging, characterized in that it consists in:supplying, in intake mode with scavenging, non-carbureted air through one (16) of the intake means then, in the vicinity of the scavenging end, in supplying carbureted air through the other (14) intake means,supplying, in intake mode without scavenging, carbureted air through the two intake means (14, 16).