The TRIAD approach achieves site-specific soil ecological risk assessments by integrating three lines of evidence (LoEs): chemistry, ecotoxicology, and ecology. Although the various toolbox items within TRIAD should be analyzed according to the site characteristics, no studies have yet determined the effect of selecting different analytical items on the resulting ecological risk. In this study, we applied the tiered TRIAD system to two heavy-metal-contaminated sites and compared the ecological risk values derived from two different soil extraction methods: batch and column tests. Although we observed no significant difference in the LoE or integrated risk values at either site, the batch test in soil extract bioassays was confirmed to be effective for old metal-contaminated sites. This study also highlights the importance of selecting toolbox items according to the site and contamination characteristics. Our analysis emphasized the need to integrate all three LoEs within the TRIAD methodology according to the site characteristics, as well as establish causality for the considerable uncertainties arising from heterogeneity among the three LoEs. This study provides practical insights for developing TRIAD guidance and improving future applications to site-specific soil ecology risk assessment.