Biogas production generates digested slurry as a by-product. It can be used as fertilizer especially after its conversion into digested liquid. A microcosm-based study was conducted in order to compare the effects of single application of digested liquid or chemical fertilizer on N2O flux and crop yield of komatsuna vegetable. Analysis revealed that digested liquid-treated soils released almost equal cumulative N2O (0.43 g N m−2) compared to chemical fertilizer (0.39 g N m−2). The uncropped soils treated with the digested liquid and chemical fertilizer released more N2O compared to corresponding cropped soils. The N2O emission factor and soil mineral N contents were similar for the digested liquid and chemical fertilizer-treated soils. Plant biomass in the first crop after digested liquid application was significantly higher (5.59 g plant−1) than that after applied chemical fertilizer (4.78 g plant−1); but there was no significant difference for the second crop. Nitrogen agronomic efficiency was improved by the digested liquid compared to chemical fertilizer. This study indicates that cumulative N2O flux was similar after application of the digested liquid and chemical fertilizer, while the overall yield from both croppings was increased in the digested liquid-treated soil compared to chemical fertilizer-treated soil.