Traditionally, biogenic volatile organic compound (BVOC) emissions are often considered a unidirectional flux, from the ecosystem to the atmosphere, but recent studies clearly show the potential for bidirectional exchange. Here we aimed to investigate how warming and leaf litter addition affect the bidirectional exchange (flux) of BVOCs in a long-term field experiment in the Subarctic. We also assessed changes in net BVOC fluxes in relation to the time of day and the influence of different plant phenological stages. The study was conducted in a full factorial experiment with open top chamber warming and annual litter addition treatments in a tundra heath in Abisko, Northern Sweden. After 18 years of treatments, ecosystem-level net BVOC fluxes were measured in the experimental plots using proton-transfer-reaction time-of-flight mass spectrometry (PTR–ToF–MS). The warming treatment increased monoterpene and isoprene emissions by ≈50%. Increasing temperature, due to diurnal variations, can both increase BVOC emission and simultaneously, increase ecosystem uptake. For any given treatment, monoterpene, isoprene, and acetone emissions also increased with increasing ambient air temperatures caused by diurnal variability. Acetaldehyde, methanol, and sesquiterpenes decreased likely due to a deposition flux. For litter addition, only a significant indirect effect on isoprene and monoterpene fluxes (decrease by ~50%–75%) was observed. Litter addition may change soil moisture conditions, leading to changes in plant species composition and biomass, which could subsequently result in changes to BVOC emission compositions. Phenological stages significantly affected fluxes of methanol, isoprene and monoterpenes. We suggest that plant phenological stages differ in impacts on BVOC net emissions, but ambient air temperature and photosynthetically active radiation (PAR) also interact and influence BVOC net emissions differently. Our results may also suggest that BVOC fluxes are not only a response to changes in temperature and light intensity, as the circadian clock also affects emission rates.