This paper deals with a control proposal for serial multicellular choppers. The proposed scheme takes advantage of the continuous and discontinuous chopper operation, and introduces the use of two Petri nets (PNs) to carry out the control action. The first PN generates the needed voltage level to assure the output reference current tracking, while a second PN solves the problem of capacitor voltage balancing, using switching state redundancies. Also, a stability analysis based on a Lyapunov function is used to ensure the convergency of the states under the commutation rule. The main advantage of this approach is the integration of the continuous and discrete dynamics through PNs, which directly drives the converter power semiconductors. Furthermore, this proposal could lay the basis for future studies in the design of converter controllers using the formal analysis tools offered by PNs. Experimental results from four and five-level choppers are used to emphasize the performance and the effectiveness of the proposed control scheme.