Here the metal-organic framework material MIL-88A is used to purify and immobilize an acyltransferase from Mycobacterium smegmatis (MsAcT) simultaneously from the broken bacterial liquid. Regarding the possibility that the MsAcT@MIL-88A may display weak stability in its application, a silica layer is further introduced around it as a “shield” to protect the enzyme from degradation. The obtained MsAcT@MIL-88A@silica can exhibit high activity recovery, excellent thermal, pH, and storage stabilities compared with those of MsAcT@MIL-88A. The MsAcT@MIL-88A@silica can also be effectively recycled, and its initial activity of 84.0 % ± 1.2 % can be retained after the 5th cycle for N-acylation reaction in water. More importantly, the MsAcT@MIL-88A@silica can display much higher catalytic activity towards the reactions between ethyl or vinyl esters and aniline than those of free MsAcT and MsAcT@MIL-88A in aqueous media. This study provides a simple and inexpensive strategy to prepare MsAcT@MIL-88A@silica with high activity, stability, and excellent recyclability, and highlights its application potential as a biocatalyst.