Soil biogenic volatile organic compounds (sBVOCs) contribute to ecosystem emissions and play an important role in the soil ecosystem. Most previous studies on sBVOCs have looked at emissions from excavated soil in the laboratory or in situ emissions from areas with bare soil, using chambers. So far, however, the actual BVOC concentrations in the soil have rarely been considered. Herein, we sought to explore the relationships between the vegetation cover in a low Arctic heath ecosystem in Western Greenland and the BVOC concentration in the soil below. In situ measurements were performed at 15‐cm depth in areas dominated by Cassiope tetragona, Empetrum nigrum, Salix glauca, and Betula nana and along a 36‐m‐long transect with mixed vegetation cover during the growing seasons of 2015–2017. sBVOC concentrations varied between the different vegetation covers, with higher concentrations below Cassiope and Betula compared to Empetrum. Furthermore, sBVOC concentrations differed along the transect, and this variation was also partly related to differences in the vegetation cover. Moreover, we demonstrate that installation of a soil probe, for sampling soil air, changes the composition and magnitude of sBVOCs up to 1 day after the installation.