The increase in greenhouse gas concentration, one of which is Methane (CH4), is the main cause of global warming and climate change. Organic materials which easily decomposed are the main sources of CH4 production in paddy fields. The research aimed to find out and analyze the dynamics of CH4 emission in each stage of rice growth, seasonal CH4 emission, and rice productivity cultivated both organically and conventionally on Alfisols and Andisols at Karanganyar Regency, Indonesia. All treatments were conducted by local farmers with common agricultural practices. In conventional farming, for Andisols only fertilizer has applied the chemical whereas for Alfisols the chemical fertilizer was applied with the addition of fresh chicken manure. The sampling of CH4 gas conducted four times in each location at 15, 35, 65, and 100 days after planting (DAP), respectively, using box chambers (50×50×100 cm). The gases were analyzed using gas chromatography, while productivity was determined by calculating total yield 2.5 m−2 (Indonesian Statistical Bureau). The treatment of Andisols C (Andisols with Conventional Farming Management) resulted in the highest CH4 emission in paddy fields for one planting season. The highest CH4 emissions were obtained at the active tillering phase (35 DAP), because of the effect of flooded conditions. For both andisols and alfisols conventional farming management resulted in higher rice productivity, whereas organic farming management resulted in better economically and in preserving the environment.