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Background  The greenhouse gas (GHG) mitigation is one of the most important environmental benefits of using bioenergy replacing fossil fuels. Nitrous oxide (N 2 O) and methane (CH 4 ) are important GHGs and have drawn extra attention for their roles in global warming. Although there have been many works of soil emissions of N 2 O and CH 4  from bioenergy crops in the field scale, GHG emissions in large area of marginal lands are rather sparse and how soil temperature and moisture affect the emission potential remains unknown. Therefore, we sought to estimate the regional GHG emission based on N 2 O and CH 4  releases from the energy crop fields.    Results  Here we sampled the top soils from two  Miscanthus  fields and incubated them using a short-term laboratory microcosm approach under different conditions of typical soil temperatures and moistures. Based on the emission measurements of N 2 O and CH 4 , we developed a model to estimate annual regional GHG emission of  Miscanthus  production in the infertile Loess Plateau of China. The results showed that the N 2 O emission potential was 0.27 kg N ha −1  year −1  and clearly lower than that of croplands and grasslands. The CH 4  uptake potential was 1.06 kg C ha −1  year −1  and was slightly higher than that of croplands. Integrated with our previous study on the emission of CO 2 , the net greenhouse effect of three major GHGs (N 2 O, CH 4  and CO 2 ) from  Miscanthus  fields was 4.08 t CO 2eq  ha −1  year −1  in the Loess Plateau, which was lower than that of croplands, grasslands and shrub lands.    Conclusions  Our study revealed that  Miscanthus  production may hold a great potential for GHG mitigation in the vast infertile land in the Loess Plateau of China and could contribute to the sustainable energy utilization and have positive environmental impact on the region.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1320-8) contains supplementary material, which is available to authorized users.

N2O and CH4 emission from Miscanthus energy crop fields in the infertile Loess Plateau of China