The soil microbial community and nitrogen (N) dynamics change seasonally due to several factors. The microbial community structure (MCS) can regulate N dynamics. However, there is insufficient information on seasonal changes in MCS and the relationship between MCS and N dynamics. We investigated MCS and N dynamics in forest soils with two different fertilities throughout a year. MCS, measured with phospholipid fatty acid (PLFA) analysis, showed a consistent seasonal trend, regardless of the fertility. Microbial indices (particularly the Saturated-/monounsaturated-PLFA ratio; Sat/mono) indicated a major PLFA shift among seasons, with temperature likely the most important factor. The fungal-/bacterial-PLFA ratio in the dormant season (December–April) was approximately 1.3 times greater than in the growing season (June–November). The trend in N dynamics showed that in summer (June–August), the gross N mineralization potential was greater than immobilization, whereas in winter (December–April), immobilization was dominant. The net mineralization potential in the growing season was approximately 1.6 times higher than in the dormant season. Moreover, a relationship was found between Sat/mono and N transformation potentials. We highlight the microbial sensitivity to seasonal dynamics which can be associated with temperature, as well as carbon and N dynamics.