As conventional geothermal energy resources are increasingly explored and exploited, there is a need to explore non-conventional geothermal energy resources for future development of geothermal energy, such as using acidic geothermal water. However, studies have shown that simple neutralization of the acidic water might bring a risk of silica scaling due to the metal contents, such as iron (Fe). Therefore, in this study, the chelating effect of ethylenediaminetetraacetate (EDTA) on Fe was examined to prevent the polymerization of silicic acid, its precipitation, and its adsorption on the surface of silica gel. Results of laboratory experiments showed that adding Fe(III) accelerated the polymerization of silicic acid when NaOH was used to adjust the pH of acidic geothermal water. On the contrary, the acceleration effect of Fe(III) was not observed when EDTA·4Na was used to adjust the pH. The concentration of monomeric Fe(III) immediately decreased to almost 0 after adding EDTA·4Na, suggesting effective Fe(III) trapping by EDTA. The results of onsite adsorption experiments agreed with the laboratory experiment, where Fe(III) accelerated silicic acid's adsorption rate on the silica gel's surface, and EDTA effectively prevented its acceleration effect. The consistent result of the onsite experiment suggests the applicability of this method to prevent the precipitation of siliceous deposits and the formation of silica scale from Fe-bearing geothermal water.