A controllable and facile strategy is established for constructing metal–organic frameworks‐based (MOF‐based) hollow composites via a protein‐induced soft‐templating pathway. Using metal‐sodium deoxycholate hydrogel as soft‐template, nanotubes are gained while the protein is absent. With the presence of protein, hollow nanospheres structure are prepared by changing the amount of protein. To verify the universality of the proposed pathway, two kinds of proteins (Burkholderia cepacia lipase and penicillin G acylase) and three kinds of MOF (ZIF‐8, ZIF‐67, and Fe‐MOF) are adopted as model proteins and materials, and the obtained protein‐containing composites (named protein@H‐MOF) possess high bioactivity and stability. This proposed strategy provides a facile method for preparing MOF‐based composites under mild conditions, facilitating the applications of MOF in the fields of biocatalyst construction, biomolecule encapsulation, and drug delivery.