•Altered mixture and structure of Alpine mixed forests delays natural regeneration.•We studied optimal gap spatiotemporal dynamics for natural regeneration.•Results indicate gap and microsite partitioning between Norway spruce and beech.•Spruce seedlings were associated with diffuse light and thick organic horizons.•Higher topsoil moisture content, proximity of seed trees favoured beech seedlings. Mixed mountain forests composed of Picea abies, Abies alba and Fagus sylvatica represent one of the most important alpine ecosystems with respect to economics, environmental effects and social functions. However, many stands are characterised by even-aged forest structure and altered tree species composition, making them more prone to disturbances and less effective in protection against natural hazards. Changes to the forest microclimate and nutrient cycling delay natural regeneration and favour the successional development of ground vegetation. In this study we hypothesized that the creation of gaps of appropriate size and shape would facilitate natural regeneration and forest conversion. In 2003, we selected 15 gaps, ranging in size from 0.01 to 0.62 ha and more than 50 years in age, and three areas below closed canopy on a south facing P. abies dominated mixed mountain forest (1380–1480 m a.s.l.). Within the gaps we established 542 systematically distributed research plots (1.5 × 1.5 m) and analysed regeneration attributes according to height classes, ground vegetation coverage, light climate, topsoil moisture, microsite relief and soil features. Measurements were repeated after five vegetation seasons and indicated minimal changes in vegetation structure and the slow development of regeneration overall. Vegetation ordination and generalized linear mixed models showed a positive association of P. abies seedling abundance with diffuse light, thickness of the organic horizons, presence of CWD and moss coverage and a negative association with ground vegetation cover, soil water content, Landolt indication value for nutrients and direct light. Fagus sylvatica seedlings were more abundant closer to seed trees, on less acidic soils with higher moisture content and on concave microrelief. The results indicate that P. abies and F. sylvatica seedlings may successfully establish under slightly open forest canopies, but in a few years the former require amounts of diffuse light comparable with that in the medium sized gaps in this study (0.15 ha). Due to the negative association between direct light and regeneration, gaps should be elliptical with the long axis oriented east-west. Recruitment of all species was significantly retarded by overbrowsing.