Stability is crucial for the practical application of heterogeneous catalysts, particularly in industrial processes, where catalyst deactivation often occurs due to factors such as sintering, poisoning, and active site degradation. This study investigates the effectiveness of utilizing covalent organic frameworks (COFs), specifically RT‐COF‐1, to enhance the stability of Cu/Fe3O4 catalysts in harsh water–gas shift (WGS) reaction environments. By encapsulating Cu/Fe3O4 with trace RT‐COF‐1, we aimed to preserve the structural integrity and active interfaces between the metal components during catalytic reactions. Characterization techniques, including X‐ray photoelectron spectroscopy, nitrogen sorption, and high‐angle annular dark‐field scanning transmission electron microscopy, confirmed the successful COF coating and its role in preventing particle aggregation and maintaining active site structures over extended catalytic tests. Notably, Cu/Fe3O4@COF demonstrated significantly enhanced stability during a continuous 24‐h WGS test compared to uncoated catalysts, which exhibited rapid deactivation. Mechanistic insights indicated that COF coating reduced the number of active sites while preserving the overall morphology of the catalyst, contributing to its robust performance. Ultimately, this work highlights the potential of COF encapsulation as an effective strategy for enhancing the durability and efficacy of multifunctional catalysts in challenging reaction conditions.