Rates of tree mortality continue to rise with climate change, particularly in high elevation subalpine forests. In these systems, which depend on a narrow range of microsite conditions for successful seedling establishment, growing drought frequency and intensity may impose regeneration bottlenecks that further exacerbate population declines. However, it is unclear how regeneration processes tied to species-specific stress tolerances and microsite preferences are affected by varying magnitudes and durations of drought. To simulate moderate (50%) and severe (100% precipitation exclusion) growing-season drought, we installed precipitation exclusion shelters in shade and canopy gap light microenvironments over naturally-regenerating seedlings across a range of size-delimited establishment cohorts spanning first year emergents to large and well-established seedlings of two dominant subalpine forest species – Engelmann spruce (Picea engelmannii Parry ex Engelmann) and subalpine fir (Abies lasiocarpa (Hook) Nutt.). Seedling survival and gas exchange physiology was assessed to test the interacting effects of drought and light microenvironment on seedling performance, with contrasts to each species’ historically preferred microsite under ambient precipitation conditions. Shade partially ameliorated drought effects when precipitation reductions were moderate as illustrated by rates of seedling mortality that were statistically indistinguishable from reference rates for both species, whereas moderate drought in canopy gaps significantly or nearly-significantly increased seedling mortality in several cohorts of both spruce and fir (1.9–2.9 and 2.3–7.5 times greater mortality risk in spruce and fir, respectively). When drought was severe, however, shade induced prolonged net-negative photosynthetic carbon assimilation as low as a −1.5 μmol CO2·m−2·s−1 (growing-season average), which occurred alongside significantly increased mortality in spruce (3.2–9.4 times greater mortality risk). In contrast, mortality was significantly higher in canopy gaps under severe drought for fir (5.5–23.1 times greater mortality risk). Larger seedling size was strongly associated with lower mortality risk and more conservative stomatal behavior (e.g., predominantly <0.1 mol·H2O·m−2·s−1 growing-season averages), illustrating the sensitivity of new seedlings to microsite environments. However, persistent declines in photosynthetic carbon uptake observed across all seedling sizes in shaded microsites suggests the potential for lagged mortality and greater susceptibility to recurring drought even for larger and seemingly well-established seedlings. These results demonstrate how acute, intense droughts may alter historical patterns of spruce-fir seedling regeneration and highlight the importance of maintaining suitable microsites when implementing adaptive management strategies to avoid regeneration bottlenecks in forests that are already vulnerable to accelerating drought-induced mortality.