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Biogenic volatile organic compound (BVOC) flux dynamics during the subarctic autumn are largely unexplored and have been considered insignificant due to the relatively low biological activity expected during autumn. Here, we exposed subarctic heath ecosystems to predicted future autumn climate scenarios (ambient, warming, and colder, dark conditions), changes in light availability, and flooding, to mimic the more extreme rainfall or snowmelt events expected in the future. We used climate chambers to measure the net ecosystem fluxes and bidirectional exchange of BVOCs from intact heath mesocosms using a dynamic enclosure technique coupled to a proton‐transfer‐reaction time‐of‐flight mass spectrometer (PTR–ToF–MS). We focused on six BVOCs (methanol, acetic acid, acetaldehyde, acetone, isoprene, and monoterpenes) that were among the most dominant and that were previously identified in arctic tundra ecosystems. Warming increased ecosystem respiration and resulted in either net BVOC release or increased uptake compared to the ambient scenario. None of the targeted BVOCs showed net release in the cold and dark scenario. Acetic acid exhibited significantly lower net uptake in the cold and dark scenario than in the ambient scenario, which suggests reduced microbial activity. Flooding was characterized by net uptake of the targeted BVOCs and overruled any temperature effects conferred by the climate scenarios. Monoterpenes were mainly taken up by the mesocosms and their fluxes were not affected by the climate scenarios or flooding. This study shows that although autumn BVOC fluxes on a subarctic heath are generally low, changes in future climate may strongly modify them. The exchange of biogenic volatile organic compounds (BVOCs) between Arctic tundra and the atmosphere is largely unexplored during the autumn because plants are inactive and unproductive at that time of the year. Here, we measured BVOC fluxes in small blocks of Arctic tundra under treatments that mimicked predicted future autumn conditions, including temperature manipulations, alongside a flooding event to mimic more extreme rainfall or snowmelt. Warming caused the tundra to release more BVOCs, due to the higher release from plants and/or soil microbes, or alternatively, to take up more BVOCs from the atmosphere. Colder and dark conditions slowed down the activity of tundra vegetation and soil microbes, resulting in a net uptake of BVOCs for all of the compounds tested. Flooding of the tundra ecosystems increased BVOC uptake, possibly because the BVOCs dissolved in water or because the water hindered plant and soil BVOC production due to saturation of the soil and the resulting lack of oxygen. Biogenic volatile organic compound (BVOC) fluxes in the autumn ecosystem are mainly derived from soil microbial activityFlooding results in negative net BVOC exchange, mainly due to BVOC depositionAutumnal warming enhances vegetation growth and soil respiration, resulting more often in net BVOC emissions than under colder conditions Biogenic volatile organic compound (BVOC) fluxes in the autumn ecosystem are mainly derived from soil microbial activity Flooding results in negative net BVOC exchange, mainly due to BVOC deposition Autumnal warming enhances vegetation growth and soil respiration, resulting more often in net BVOC emissions than under colder conditions