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Research background. Barberry juice is a rich source of bioactive compounds and shows different health properties such as antioxidant and anticancer activities. Clarification, as the removal process of suspended material, is an important step in production process of fruit juice due to its significant effect on the appearance, flavor and commercialization of juice. Pectinase is the most important enzyme applied in juice clarification that breaks down the pectin polymer structure and leads to reduce the undesirable turbidity. Pectinase immobilization is a way to overcome free enzyme drawbacks such as instability, high cost, the difficulty of recovery and recyclability. Also, continuous clarification process which is highly preferred in fruit juice industry is not possible without enzyme immobilization. Experimental approach. Pectinase enzymes were immobilized on the functionalized glass beads (glass bead+3-aminopropyl triethoxysilane) by glutaraldehyde, polyaldehyde pullulan and polyaldehyde kefiran and the barberry juice clarification was accomplished in the batch and continuous process in a packed bed reactor (PBR). Also, the effect of clarification process on the physicochemical and antioxidant properties of the barberry juice samples was evaluated. Results and conclusions. The clarification optimum conditions in the PBR were obtained at a flow rate of 0.5 mL/min, the temperature of 50 °C and treatment time of 63 min. The clarification process led to a decrease in turbidity, pH, total soluble solids, viscosity, total phenol content and antioxidant activity of the juice samples. Also, this process increased the clarity, acidity, reducing sugar content and the lightness parameter of the barberry juice. It was found that the greatest effect on the studied properties was related to polyaldehyde kefiran-immobilized pectinase treatment in the continuous process and both new cross-linkers had better enzyme immobilization performance than common cross-linker (glutaraldehyde). Novelty and scientific contribution. For the first time, barberry juice was clarified with pectinase immobilized by polyaldehydes of pullulan and kefiran and the obtained results showed that the pectinase immobilization by these new cross-linkers was much more efficient than by the glutaraldehyde as common cross-linker. Therefore, it seems that these findings can be of use towards an industrialised production of fruit juices.