The greenhouse-gas (GHG) balance of CH4 and N2O emissions and CO2 respiration in peatlands plays a key role in climate change. A GHG balance is mostly calculated from point measurements. In this study we propose and test a geophysical method of low frequency domain electromagnetic method (FDEM) as a proxy for forest-floor CO2 respiration and CH4 emissions in two 50 × 100 m drained peatlands in Estonia: a Downy birch and a Scots pine stand from April to September 2015. The FDEM measurement campaign in September 2015 yielded a detailed map of topsoil electrical conductivity. We explain the predictive power of FDEM on GHG emissions through relationships with dry bulk density of soil. Although we over- or underestimated some fluxes owing to soil heterogeneity, we composed reasonably credible GHG emission maps. The initial results seem promising and we recommend further application of FDEM methods. Display omitted •We tested the FDEM as proxy for CO2 and CH4 emissions in drained peatlands.•FDEM correlates with CO2 production and CH4 fluxes.•Upscaling point CH4 fluxes into an annual sequence of detailed maps.•FDEM is a promising tool for mapping GHG emissions.