Phthalate esters (PAEs), widely used as plasticizers, pose severe environmental and health risks. This study investigated the enzymatic hydrolysis of PAE congeners (dibutyl phthalate (DBP) and diethylhexyl phthalate (DEHP)) in aqueous and soil systems using Bacillus subtilis esterase and a new thermoalkaliphilic Geobacillus sp. esterase. A novel esterase secreted from Geobacillus sp. which was isolated from a geothermal region (Türkiye) was expressed in E.coli and purified. Geobacillus sp. esterase was able to degrade almost 30% of DBP and 40% of DEHP (100 mg/L) in the aqueous system within 336 h, while it degraded virtually 59% and 98% of DBP in agricultural area soil (soil-1) and forest area soil (soil-2), respectively, at the same time. To compare with Geobacillus sp. esterase, Bacillus subtilis esterase was used, which fully degraded DBP with 100 mg/L in the soil-1 and soil-2 for 72 h and 2 h, respectively. The performances of both esterases to degrade DEHP (100 mg/L) were similar in soil-1 (∼35%) and soil-2 (∼50%) for 336 h. Soil characteristics significantly influenced PAE degradation. Compared to that in the aqueous system, Geobacillus sp. esterase in soil systems had a higher degradation efficiency. This was likely due to its origin from a soil microorganism. Variations in the degradation ability of two enzymes most probably arose from substrate specificities and enzyme dynamics. Molecular docking results showed that DBP had a higher affinity to both enzymes than DEHP. Overall, this study offers important evidence that Bacillus subtilis esterase and Geobacillus sp. esterase are effective biocatalysts for removing the pollutants with ester bonds in the environment.