Ex-situ measurement of soil respiration is usually done with highly disturbed samples that may confound the interpretation and extrapolation of results. We have developed a lab respiration assessment method that better simulates field conditions and allows efflux estimations based on soil surface area. First, intact soil cores are extracted in the field and transferred to the lab. Next, soil moisture content and bulk density are assessed in each soil core. Immediately following this the soil cores are gently broken, pooled per treatment (or plot) and the root systems removed. Subsequently the field moist, non-sieved soils are repacked into microcosm cores at their respective bulk densities. Moisture content in the microcosms is adjusted to desired levels by adding drops of deionized water or by air drying for several hours. After moisture adjustment, the cores are pre-incubated at 25 °C for two weeks. Afterwards, the microcosms are further incubated in the dark at the desired temperatures in airtight containers. At incubation times of 0, 48 and 96 h, 20 ml of gas sample is collected from each container via the septum, and then injected into pre-evacuated exetainers for CO2 determination using a gas chromatograph or an infrared gas analyzer. Finally, soil efflux is estimated based on the rate of linear CO2 increase in the container headspace. One of the advantages of this method is that results can be presented per unit of mass (e.g. mg CO2-C g soil-1 day-1) or area (e.g. g CO2-C m2 day-1). These soil microcosms can also be used to simultaneously assess emissions of CH4 and N2O during incubations. This new method uses: •Small intact soil cores collected in the field.•Soil microcosms.•Efflux calculated per unit of area.