As a functional low-calorie sugar, d-allulose demonstrates significant potential for applications in the food industry. Ketose 3-epimerases (KE) catalyzing the epimerization of d-fructose into d-allulose, play a critical role in the production of d-allulose. Majority of the reported KE exhibited maximum activity at high temperatures (60–70 °C) and pH (7.5–8.0) with metal ions (Mn2+ or Co2+), resulting in browning reaction and complex processes (adjusting pH of fructose solution, removing heavy metal ions, etc.) in allulose production. In this study, a novel d-allulose 3-epimerase from B. cihuensis (BcDAE) was identified and characterized. The BcDAE showed maximum activity at 40–50 °C and pH 7.0, alongside exhibiting board pH tolerance in weakly acidic environments. As a mesophilic enzyme, BcDAE could provide advantages by mitigating browning reactions of substrate and product, minimizing by-product formation, and reducing energy consumption during production. Robustness in acidic environments of BcDAE might renders the enzyme well-suited for fructose conversion without pH adjustments. Considering the poor thermostability and dependence on Mn2+ of BcDAE, the enzyme was captured in Mn-BTC MOF material using a straightforward co-precipitation method. The MOF-based enzyme was subsequently encapsulated to form micrometer-sized immobilized enzyme PDA@BcDAE@Mn-BTC using polydopamine as the cross-linker. Metal ions are not required in the reaction using the immobilized BcDAE. Significantly, after 10 repeated usage cycles, the immobilized BcDAE maintained a relative enzyme activity exceeding 70%, surpassing the performance of other reported immobilized DAE within MOF. Furthermore, comprehensive characterization of the immobilized BcDAE confirmed the success and feasibility of the immobilization strategy.