Biotransformation with the help of enzymes can greatly improve the rate and stereospecificity of reactions in organic chemistry. However, the use of organic solvents and harsh conditions in biotechnological applications often correlates with enzyme deactivation or a dramatic drop in catalytic activity. Detailed molecular understanding of the protein structure and conformational dynamics allows us to address such limitations and to finely tune catalytic activity by modifying the solvent, the support, or the active site of the enzyme. Along with physico-chemical methods of enzyme stabilization, such as additive approach, chemical modification, and immobilization of enzymes, approaches of enzyme engineering based on DNA recombination can be used to enhance the performance of biocatalysts. Since successful synthetic and industrial applications of biocatalysts require systems that are not only stable and active, but can also be reused in a continuous flow process reducing the production cost, the goal of this chapter is to introduce the reader to the vast scope of techniques available for enzyme improvement, highlighting their opportunities and limitations for the real-world technological processes.