Natural gas is well-suited as a fuel in the transport sector. Due to its excellent combustion characteristics, engines operating with compressed natural gas (CNG) reach high efficiency, especially if operated at lean conditions. However, CNG engine research mainly focusses on stoichiometric conditions in order to use a three-way catalytic converter for the exhaust gas after treatment system. With the objective to explore the potential of CNG engines operated at lean conditions, a turbo-charged CNG engine with high com-pression ratio is developed and optimized for lean operation. In order to increase the ignition energy, the CNG engine is equipped with scavenged pre-chambers. A specific control structure is developed, which allows to operate the engine at a pre-defined (lean) air-to-fuel ratio. Further functionalities such as the combustion placement control and algorithms to estimate the conditions inside of the pre-chamber are implemented. The first part of this paper describes this engine control structure, which is specifically developed for the lean-burn CNG engine. In the second part, the effects of pre-chamber scavenging on engine performance criteria such as the combustion stability, engine efficiency or engine emissions are analyzed. With the objective to use pre-chamber scavenging to improve engine performance, a scavenging feed-back control strategy is proposed. In order to control the ignition delay, this strategy adapts the amount of CNG injected into the pre-chamber with a linear controller or an extremum seeking algorithm depending on the air-to-fuel ratio of the main chamber.