• A universal ‘one-stone-two-bird’ enzymatic surface functionalization strategy was proposed. • A unique ZIF-L with 15 nm mesopore was obtained due to competitive coordination. • Undesirable interfacial interaction between ZIF-L and enzyme was blocked by hydrophilic polymers. • ZIF-L@HRP-PAA increased activity by 2–23 times. • ZIF-L@enzyme-PAA has an excellent tolerance to harsh environments. Herein, we present a facile strategy for simultaneously solving two significant difficulties in metal-organic framework (MOF)-enzyme complexes: limited substrate accessibility and unfavorable interfacial interactions between MOFs and enzymes. We exploited the profound effect of the protein surface on the MOF structure and grafted short-chain polyacrylic acid (PAA) onto the enzyme surface to improve the microenvironment of the enzyme confined inside the MOF. PAA not only created mesopores inside the MOF via competitive coordination but also served as a protective layer to reduce the influence of interfacial interactions on enzyme conformation. Benefitting from this “one-stone-two-bird” approach, the activity of the enzyme-PAA complexes encapsulated in a zeolitic imidazolate framework (ZIF-L) was 2–23 times higher than that of the unconjugated enzyme in ZIF-L. Additionally, mesoporous enzyme-PAA@ZIF-L (∼15 nm) was able to endure extreme conditions and was reusable because of the shielding and confinement effects. This enzyme immobilization strategy was applied to several enzymes, and the obtained MOF-enzyme complexes showed great promise in the selective biodegradation of harmful dye molecules and point-of-care glucose detection.