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In the present communication, the simultaneous co-immobilization by covalent binding of lipase A from Candida antarctica (CALA) and lipase B from Candida antarctica (CALB) in glutaraldehyde (GLU) activated chitosan (CHI) was optimized using the Taguchi method. Under optimized conditions (pH 9, 5 mM, 6:1 (protein load/g of support and 1 h), it was possible to reach 80.00 ± 0.01% for the immobilization yield (IY) and 46.01 ± 0.35 U/g for the activity of the derivative (AtD); in this case, load protein and ionic strength were the only statistically significant parameters and, therefore, those that most influenced the immobilization process. Furthermore, at pH 7, CALA-CALB-CHI had a half-life 2–6 times longer than the mixture of CALA and CALB for a temperature range of 50−80 °C. CALA-CALB showed the highest activity at pH 7, whereas CALA-CALB-CHI, except at pH 7, was more active than the soluble lipase mixture in the pH range (5–9), especially at pH 9. CHI, CHI-GLU, and CALA-CALB-CHI were characterized by X-ray powder diffraction (XRPD), Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscope (SEM), Thermogravimetry (TGA), and Energy Dispersive Spectroscopy (EDS), proving the immobilization of CALA and CALB in chitosan. CALA-CALB-CHI derivative evaluated in the kinetic resolution of halohydrins acetates rac-2-bromo-1-(2-chlorophenyl) ethyl acetate (2a) and rac-2-chloro-1-(2,4-dichlorophenyl) ethyl acetate (2b), to produce the corresponding halohydrins 3a-b, which are intermediates in the synthesis of the drugs chlorprelanine (antiarrhythmic) and luliconazol (antifungal), respectively. (S)-bromohydrin 3a was obtained with 79% enantiomeric excess (ee), whereas (S)-chlorohydrin 3b produced with 98% ee, conversion of 46% and E > 200. Additionally, molecular docking was performed to elucidate the hydrolysis interaction reaction between β-halohydrin acetates and lipases CALA-CALB.