Many studies have examined the application of soil amendments, including pH change-induced immobilizers, adsorbents, and organic materials, for soil remediation. This study evaluated the effects of various amendments on trace element stabilization and phytotoxicity, depending on the initial soil pH in acid, neutral, and alkali conditions. As in all types of soils, Fe and Ca were well stabilized on adsorption sites. There was an effect from pH control or adsorption mechanisms on the stabilization of cationic trace elements from inorganic amendments in acidic and neutral soil. Furthermore, acid mine drainage sludge has shown great potential for stabilizing most trace elements. In a phytotoxicity test, the ratio of the bioavailable fraction to the pseudo-total fraction significantly affected the uptake of trace elements by bok choy. While inorganic amendments efficiently decreased the bioavailability of trace elements, significant effects from organic amendments were not noticeable due to the short-term cultivation period. Therefore, the application of organic amendments for stabilizing trace elements in agricultural soil requires further study.