Vietnam is one of the world’s top two rice exporting countries. However, rice cultivation is the primary source of agriculture’s greenhouse gas (GHG) emissions in Vietnam. In particular, strategies are required to reduce GHG emissions associated with the application of organic and inorganic fertilisers. The objective of this study was to assess the effects of various combinations of biochar (BIOC), compost (COMP) and slow-release urea (SRU) on methane (CH4) and nitrous oxide (N2O) emissions. In total, 1170 gas samples were collected from closed gas chambers in rice paddies at Thinh Long commune and Rang Dong farm in northern Vietnam between June and October 2014. The gas samples were analysed for CH4-C and N2O-N fluxes using gas chromatography. The application of BIOC alone resulted in the lowest CH4 emissions (4.8–59 mg C m−2 h−1) and lowest N2O emissions (0.15–0.26 µg N m−2 h−1). The combined application of nitrogen–phosphorus–potassium (NPK) + COMP emitted the highest CH4 (14–72 mg C m−2 h−1), while ½NPK + BIOC emitted the highest N2O (1.03 µg N m−2 h−1 in the TL commune), but it was the second lowest (0.495 µg N m−2 h−1) in the RD farm. Green urea and orange urea reduced N2O emissions significantly (p < 0.05) compared to white urea, but no significant differences were observed with respect to CH4 emissions. SRU fertilisers and BIOC alone measured the lowest greenhouse gas intensity, i.e. <2.5 and 3 kg CO2 eq. kg−1 rice grain, respectively. Based on these results, application of fertilisers in the form of BIOC and/or orange or green urea could be a viable option to reduce both CH4 and N2O emissions from rice paddy soils.