Phthalate esters (PAEs) stand out as the priority toxicants due to their carcinogenic, mutagenic, and teratogenic properties. The enzymatic degradation is hailed for its recognized safe and environmentally friendly properties. This study delved into PAEs’ degradation, especially dibutyl phthalate (DBP) and diethylhexyl phthalate (DEHP) by recombinant esterase from Geobacillus sp. isolated from Balçova Geothermal region in İzmir. The esterase exhibited efficient degradation of DBP but had limited effectiveness in degrading DEHP. Many experiments were conducted to compare the ability of recombinant esterase to degrade DBP and DEHP with that of commercially available enzymes secreted from various microorganisms. Among these enzymes, Bacillus subtilis esterase and Rhizomucor miehei lipase had the highest ability. They were immobilized on halloysite nanotubes (HNTs) by adsorption method to enhance their stability and prolong their activity in applications. To investigate the impact of immobilization methods, two bionanocomposites were formed by immobilization of Bacillus subtilis esterase to HNTs with chitosan (CTS) and alginate (ALG) by the cross-linking method. Two fixed-bed reactors with CTS-HNT-EST and ALG-HNT-EST were operated in batch and continuous modes for PAEs’ degradation. CTS-HNT-EST exhibited superior efficacy and durability in PAEs’ removal for both modes. Lastly, bioremediation experiments were conducted in PAEs-contaminated soils using Bacillus subtilis esterase and recombinant esterase. Although both esterase had the same active site triad, recombinant esterase had a less significant effect on PAEs’ degradation. This fact can be attributed to different substrate specificity and enzyme dynamics. Despite variations in their degradation capabilities, both commercial and newly engineered recombinant enzymes demonstrate considerable potential for breaking down PAEs.