Methane (CH4) emission from paddy rice fields is a global concern; however, engineering plant spacing can decrease CH4 emission. Due to this, field research was conducted to measure CH4 emissions from rice fields planted using jarwo 2:1 spacing, which has a 25 × 12.5 cm and 50 cm for the plant-free area (PFA), compared to tegel, which has a spacing of 25 × 25 cm. Each field was treated with organic fertilizer (mixture of cow manure and neem compost in a ratio of 1:1) with one of four doses: 0, 3, 6 and 9 tons/ha. The results showed that chemical properties such as soluble-Fe, soil organic matter (SOM), soil acidity (pH), and redox potential (Eh) were significantly correlated with CH4 emissions (0.52***, 0.47**, 0.36*, and-0.27* respectively). Jarwo 2:1 had lower CH4 emissions than tegel on all doses of fertilizer. The most efficient dose of fertilizer was 3 tons/ha applied jarwo 2:1 because it was able to produce rice up to 12 tons/ha with CH4 emissions of only 34 kg/ha/season, while CH4 emissions in tegel was 39 kg/ha/season. It is concluded that jarwo 2:1 with 3 tons/ha organic fertilizers can be recommended to farmers because it produces lower CH4 emissions and higher rice yield.