Enzymes are powerful biocatalysts but suffer from a loss of activity under harsh conditions. In this study, we developed a one-pot aqueous synthesis of enzyme-encapsulated covalent organic frameworks (COFs) to enhance both the stability and reusability of enzymes and provided a detailed analysis of enzyme-COF interactions. We successfully encapsulated β-glucosidase (BGL), alkaline phosphatase (ALP), and eight other enzymes and proteins within the TpAzo COF. Solid-state 2D NMR correlation spectroscopy provided direct molecular-level evidence of interactions between the enzyme and COF backbone, confirming structural integrity and encapsulation efficiency. Scattering-type scanning near-field optical microscopy (s-SNOM) and nanoscale Fourier-transform infrared spectroscopy (nanoFTIR) further validated the presence of BGL within the COF. The encapsulated BGL and ALP retained their catalytic activity with recyclability for up to ten cycles. Notably, the COF enhanced BGL's stability against denaturation in aqueous sodium dodecyl sulfate (SDS) solutions across a concentration range of 1-15% (w/v). This work establishes a strategy for enzyme encapsulation, leveraging enzyme-COF interactions to improve stability under extreme conditions.