Enzyme encapsulation is an attractive method among the different immobilization strategies to improve the reusability and stability of enzymes because it can separate enzymes from a hazardous external environment. However, current encapsulation methods have limitations including enzyme leakage. In this study, a new approach based on a two-step soft templating method has been proposed to encapsulate lipase within substrate permeable mesoporous silica yolk-shell spheres. In the first step, lipase was immobilized onto epoxy functionalized silica nanospheres that serve as the core materials. The core materials were mixed with a fluorocarbon surfactant, FC4, to form a core-vesicle complex. In the second step, a mesoporous silica shell was assembled surrounding the core-vesicle complex to form the yolk-shell structure with the lipase encapsulated. The mesoporous silica shell has a pore size of 2.1 nm, which is permeable to the reactant and product while isolating the enzymes from harmful external conditions. The encapsulated lipase retained 87.5% of its activity after thermal treatment at 70 C for 2 hours while the free enzyme lost 99.5% of its activity under the same treatment. Importantly, the encapsulated lipase shows significantly enhanced resistance to degradation by proteases.