Bilberry spruce forests are the most widespread forest type in the European boreal zone. Limiting the clear-cuttings size leads to fragmentation of forest cover and the appearance of large areas of ecotone complexes, composed of forest (F), a transition from forest to the cut-over site under tree canopy (FE), a transition from forest to the cut-over site beyond tree canopy (CE), and the actual clear-cut site (C). Natural regeneration of woody species (spruce, birch, rowan) in the bilberry spruce stand—clear-cut ecotone complex was studied during the first decade after logging. The effects produced by the time since cutting, forest edge aspect, and the ground cover on the emergence and growth of trees and shrubs under forest canopy and openly in the clear-cut were investigated. Estimating the amount and size of different species in the regeneration showed FE and CE width to be 8 m—roughly half the height of first-story trees. Typical forest conditions (F) feature a relatively small amount of regenerating spruce and birch. The most favorable conditions for natural regeneration of spruce in the clear-cut—mature bilberry spruce stand ecotone are at the forest edge in areas of transition both towards the forest and towards the clear-cut (FE and CE). Clear-cut areas farther from the forest edge (C) offer an advantage to regenerating birch, which grows densely and actively in this area.