Biogenic volatile organic compound (BVOC) emissions are important in the global atmospheric chemistry and their feedbacks to global warming are uncertain. Global warming is expected to trigger vegetation changes and water table drawdown in boreal peatlands, such changes have only been investigated on isoprene emission but never on other BVOCs. We aimed at distinguishing the BVOCs released from vascular plants, mosses and peat in hummocks (dry microsites) and hollows (wet microsites) of boreal peatland microcosms maintained in growth chambers. We also assessed the effect of water table drawdown (−20cm) on the BVOC emissions in hollow microcosms. BVOC emissions were measured from peat samples underneath the moss surface after the 7-week-long experiment to investigate whether the potential effects of vegetation and water table drawdown were shown. BVOCs were sampled using a conventional chamber method, collected on adsorbent and analyzed with GC–MS. In hummock microcosms, vascular plants increased the monoterpene emissions compared with the treatment where all above-ground vegetation was removed while no effect was detected on the sesquiterpenes, other reactive VOCs (ORVOCs) and other VOCs. Peat layer from underneath the surface with intact vegetation had the highest sesquiterpene emissions. In hollow microcosms, intact vegetation had the highest sesquiterpene emissions. Water table drawdown decreased monoterpene and other VOC emissions. Specific compounds could be closely associated to the natural/lowered water tables. Peat layer from underneath the surface of hollows with intact vegetation had the highest emissions of monoterpenes, sesquiterpenes and ORVOCs whereas water table drawdown decreased those emissions. The results suggest that global warming would change the BVOC emission mixtures from boreal peatlands following changes in vegetation composition and water table drawdown.