Sargassum horneri that seasonally enters East Asian waters frequently leads to negative economic consequences. Traditionally, seaweed drifts have been used as fertilizers in certain coastal areas in Korea, but there have been no scientific reports regarding this kind of application of seaweeds. Hence, this study attempted to use Sargassum as a soil amendment by monitoring soil property and microbiome changes and soybean growth. Our results suggested that the addition of S. horneri biomass to soil improved soil physicochemical properties such as CEC levels leading to more soil fertility. As and Cd concentration increases were notable in the soil, but all the metal levels were well below the Korean soil quality standards for agricultural uses. Diversity index results indicated that fungal and bacterial diversities were affected by the amount of Sargassum added. Our study demonstrated that seasonal drifts of S. horneri could be used as an excellent soil amendment. Glycine max cultivation experiments suggested that 4% was the optimal amount to enhance soybean growth in agricultural practice. Unfortunately, clear differentiation in species diversity affected by each experiment was not observed in this study. Nonetheless, we were able to identify some positive and negative correlations of the certain microbial groups (U. isabellina, R. delemar, T. harzianum, and P. aryabhattai) with the specific metals (As and Cd) and soil elements (TP, EC, and salinity) possibly originated from S. horneri. Their biological functions should be carefully monitored when S. horneri drift is buried in agricultural soil.