The projected increase in the availability of gaseous fuels by growing popularity of household natural gas (NG) filling stations and the increase in the production of gaseous biogas-derived fuels is conducive to an increase in the use of NG fuel. Currently, natural gas in various forms (compressed natural gas (CNG), liquefied natural gas (LNG)) is popular in maritime, rail and road transport. A new direction of natural gas application may be non-road mobile machines powered by a small spark-ignition engine (SI). The use of these engines in the wood chippers can cause the reduction of machine costs and emissions of harmful exhaust gases. In addition, plant material chippers intended for composting in bio-gas plants can be driven by the gas they are used to produce. The biogas can be purified to bio-methane to meet natural gas quality standards. The article presents the design of the natural gas supply system, which is an upgrade of the Lifan GX 390 combustion engine spark ignition engine (Four-stroke, OHV (over head valve) with a maximum power of 9.56 kW), which is a common representative of small gasoline engines. The engine is mounted in a cylindrical chipper designed for shredding branches with a maximum diameter of up to 100 mm, which is a typical machine used for cleaning work in urban areas. The engine powered by CNG and traditionally gasoline has been tested in real working conditions, when shredding cherry plum (Prunus cerasifera Ehrh. Beitr. Naturk. 4:17. 1789 (Gartenkalender4:189–204. 1784)). Their diameter was ca. 80 mm, 3-metere-long, and humidity content ca. 25%. The systems were tested under the same actual operating conditions, the average power generated by the drives during shredding is about 0.69 kW. Based on the recorded results, it was found that the CNG-fuelled engine was characterized by nitrogen oxides (NOx) emissions higher by 45%. The other effects of CNG were a reduction in carbon dioxide (CO2), carbon monoxide (CO) and hydrocarbon (HC) emissions of about 81%, 26% and 57%, respectively. Additionally, the use of CNG reduced fuel consumption by 31% and hourly estimated machine operating costs resulting from fuel costs by 53% (for average fuel price in Poland: gasoline: 0.99 EUR/L and CNG: 0.71 EUR/m3 on 08 November 2020). The modernization performed by the authors ensured the work of the drive unit during shredding, closer to the value of stoichiometric mixtures. The average (AVG) value of the air fuel ratio (AFR) for CNG was enriched by 1.2% (AVG AFR was 17), while for the gasoline engine the mixture was more enriched by 4.8% (AVG AFR was 14). The operation of spark-ignition (SI) combustion engines is most advantageous when burning stoichiometric mixtures due to the cooperation with exhaust aftertreatment systems (e.g., three-function catalytic converter). A system powered by CNG may be beneficial in systems adapting to operating conditions, used in low-power shredding machines, whose problem is increased HC emissions, and CNG combustion may reduce them. The developed system does not exceed the emission standards applicable in the European Union. For CO emissions expressed in g/kWh, it was about 95% lower than the permissible value, and HC + NOx emissions were 85% lower. This suggests that the use of the fuel in question may contribute to tightening up the permissible emission regulations for non-road machinery.