Regeneration of Picea abies in high-elevation mountain forests often depends on the presence of coarse woody debris (CWD), as logs provide sites with more favorable conditions for spruce regeneration compared to the forest floor. However, there is little quantitative knowledge on the factors that are conducive to or hindering spruce establishment on CWD. We examined spruce regeneration on CWD by sampling 303 plots (50 cm × 50 cm each) on 56 downed logs in a virgin forest in the Swiss Alps. Variables describing microsite conditions were measured, and fungi were isolated from wood samples. To investigate the relationship between the ecological factors and establishment success, two models were fitted with seedling and sapling density as response variables, respectively. Besides log diameter, the models identified different ecological factors as significant for seedling and sapling establishment, i.e., regeneration depends on different factors in different development stages. Seedling density depended on the type of rot, log inclination, and decay stage. Sapling density depended mainly on light availability, cover by bark and moss, the time of tree fall, and the distance between the log surface and the forest floor. A total of 22 polypore fungi were isolated from the wood samples, four of them being threatened species. White- and brown-rot fungi were found in all decay stages. The visual assessment of the type of rot in the field corresponded in only 15% of cases to the type of rot caused by the isolated fungi; hence caution is needed when making field assessments of rot types.