Poultry-litter biochar and Azolla as green manure amendments are reported to enhance paddy soil fertility and rice yields. However, whether their co-application in lowland rice paddies has synergistic effects and whether those benefits are accompanied by greenhouse gas (GHG) emissions remains unknown. The objective of this study was to determine the effects of poultry-litter biochar (hereafter: biochar) and its co-application with Azolla as green manure (hereafter: Azolla), on the simultaneous methane (CH
4
) and nitrous oxide (N
2
O) emissions from a lowland paddy soil planted with rice during a single rice growing season in Tsuruoka, Yamagata, Japan. Biochar and Azolla amendments were applied once before rice was transplanted at a density of 20 t ha
−1
and 133.9 kg N ha
−1
, respectively. Compared with NPK, NPK + biochar, and Azolla only treatments, Azolla and biochar co-application (i.e., Azolla + biochar) significantly increased CH
4
emissions by 33%–197.6% in the early stages of rice growth (before 63 days after transplanting, DAT), but did not significantly influence CH
4
emissions at both late rice growth stages (after 63 DAT,) and whole rice growth period (112 DAT). Conversely, Azolla + biochar significantly reduced N
2
O emissions by 83.0%–97.1% before 63 DAT, and by 76.4%–95.9% during the whole rice growth period at 112 DAT, with a significantly high interaction between biochar and fertilizer amendments. There were no significant N
2
O emission differences among all treatments after 63 DAT. Additionally, Azolla + biochar significantly increased rice grain yield by 27.3%–75.0%, and consequently, decreased both yield-equivalent CH
4
emissions by 24.7%–25.0% and N
2
O emissions by 81.8%–97.7%. Our findings suggest that the co-application of poultry-litter biochar and Azolla as green manure offers a novel approach to increase rice yield while reducing the emissions of non-carbon dioxide greenhouse gases.