Recently, zeolitic imidazolate frameworks (ZIFs) with tunable pore sizes and large surface areas have been widely used as effective supports for enzyme immobilization. A bienzyme system for the biosynthesis of L-alanyl-L-glutamine (Ala-Gln) with effective ATP regeneration was established in this study. Cells (E. coli BL21 (DE3)) expressing L-amino acid ligase (Lal) from Bacillus altitudinis (BABD) and polyphosphate kinase (PPK) were immobilized on ZIF-8 using a one-step molecular organic framework (MOF)-embedded approach. The immobilized bienzyme system, named BP@ZIF-8, was successfully fabricated and characterized using Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), and scanning electron microscopy (SEM). The resulting BP@ZIF-8 exhibited high thermostability at 50 °C and high pH stability in neutral and alkaline reaction buffers. BP@ZIF-8, for example, lost little activity after 150 minutes in carbonate buffer solution (pH 10.0). However, BP@ZIF-8 displayed poor pH stability in acidic environments. Furthermore, after seven successive uses, it still maintained 58.9% of their initial activity, exhibiting satisfactory reusability. After 14 hours, the yield of Ala-Gln catalysed by BP@ZIF-8 was around 14.56 mM, which represented an increase of roughly 14.3% above that catalysed by free cells. These findings showed that BP@ZIF-8 has a great deal of potential for practical Ala-Gln biosynthesis.