Abstract Climate warming is expected to shift bioclimatic zones and plant species distribution. Yet, few studies have explored whether seedling establishment is a possible bottleneck for future migration and population resilience. We test how warming affects the early stages of seedling establishment in 10 plant species in subarctic tundra. To zoom into the life phases where the effects of warming actually take place, we used a novel approach of breaking down the whole-season warming effect into full factorial combination of early-, mid-, and late-season warming periods. Seeds were sown in containers placed under field conditions in subarctic heath and were exposed to 3°Celevation of surface temperature and 30% addition of summer precipitation relative to ambient. Heating was achieved with Free Air Temperature Increase systems. Whole-season heating reduced germination and establishment, significantly in four out of 10 species. The whole-season warming effect originated from additive effects of individual periods, although some of the periods had disproportionally stronger influence. Early-germinating species were susceptible to warming; the critical phases were early summer for germination and mid summer for seedling survival. Graminoids, which emerged later, were less susceptible although some negative effects during late summer were observed. Some species with intermediate germination time were affected by all periods of warming. Addition of water generally could not mitigate the negative effects of whole-season heating, but at individual species level both strengthening and amelioration of these negative effects were observed. We conclude that summer warming is likely to constrain seedling recruitment in open micro sites, which is a common seed regeneration niche in tundra ecosystem. Importantly, we described both significant temporal and species-specific variation in the sensitivity of seedling establishment to warming which needs to be taken into consideration when modelling population dynamics and vegetation transitions in a warmer climate.