An analysis of soil chemical properties and microbial community compositions in spring, summer, and autumn over a growing season was conducted at three tea farms managed using the same cultivation method on Jeju Island, Korea. The contents of SOM (soil organic matter), TC (total C), TN (total N), TS (total S), potassium (K+), and lithium (Li+) increased from spring to autumn, and significant differences were observed among tea farms. Across all tea farms, the dominant bacterial phyla were Gammaproteobacteria (25.84 ± 1.66%), Alphaproteobacteria (17.99 ± 0.51%), Actinobacteria (18.38 ± 1.29%), and Acidobacteria (14.49 ± 0.79%), and the dominant fungal phyla were Ascomycota (45.16 ± 1.57%), Basidiomycota (26.76 ± 1.79%), and Mortierellomycota (23.59 ± 2.43%). We found distinct differences in the composition of the bacterial community among tea farms, whereas strong seasonal variations were observed in the composition of the fungal community. Important factors in determination of the bacterial relative abundance included water content, SOM, soil pH, EC (electrical conductivity), and contents of DOC (dissolved organic C), ammonium (NH4+), calcium (Ca2+), K+, and magnesium (Mg2+); however, only EC, DOC, and nitrate (NO3−) were important factors in the fungal relative abundance. The differences in soil chemical properties and microbial community compositions among tea farms could be attributed to the differences in environmental factors depending on the geographic location of tea farms. Seasonal variations in the contents of chemical components of tea leaves, such as catechins, total amino acids, theanine, and caffeine, were greater than the differences among the farms. The quality parameters of tea showed significant correlation with soil fungal diversity indices, indicating the possibility for use of soil fungal diversity as a biological indicator of tea quality.