The paper presents a 1D-3D numerical model to simulate the scavenging and combustion processes in a small-size spark-ignition two-stroke engine. The engine is crankcase scavenged and can be operated with both gasoline and Natural Gas (NG). The analysis is performed with a modified version of the KIVA3V code, coupled to an in-house developed 1D model. A time-step based, two-way coupled procedure is fully described and validated against a reference test. Then, a 1D-3D simulation of the whole two-stroke engine is carried out in different operating conditions, for both gasoline and NG fuelling. Results are compared with experimental data including instantaneous pressure signals in the crankcase, in the cylinder and in the exhaust pipe. The procedure allows to characterize the scavenging process and quantify the fresh mixture short-circuiting, as well as to analyze the development of the NG combustion process for a diluted mixture, typically occurring in a two-stroke engine. Results in terms of performance and emission characteristics of this engine are presented and discussed.