Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor.