Penicillin G acylase (PGA), a crucial biocatalyst in β-lactam antibiotic synthesis, has been significantly limited in its industrial application due to inherent stability issues. To address this critical challenge, efficient immobilization strategies and suitable carriers should be thoroughly investigated and developed. In this study, a novel dynamic exchange strategy was successfully implemented to immobilize PGA onto Zr-based metal-organic frameworks (Zr-MOFs), resulting in the fabrication of a series of PGA-enzyme composites (PGA@Zr-MOFs). These composites exhibited remarkable stability while retaining 61%–85% of the free enzyme activity. The PGA@Zr-MOFs demonstrated exceptional catalytic performance in fixed-bed reactors under continuous operation conditions, maintaining 99% of their initial activity after 50 consecutive cycles. Furthermore, a cost-effective solid-phase mechanical ball milling approach was developed for the synthesis of Zr-MOFs, which achieved comparable performance to previously mentioned materials. The versatility of this immobilization strategy was further demonstrated with oxidoreductases (formate dehydrogenase (FDH) and alcohol dehydrogenase (ADH)), which are essential enzymes in β-lactam antibiotic production. The immobilized oxidoreductases retained 51%–55% of their free enzyme activity and maintained 97% of their activity after 50 continuous cycles in fixed-bed operations. This strategy offers a promising platform for the eco-friendly and sustainable industrial production of β-lactam antibiotics.