We present the concept of multifunctional nanoengineered polymer capsules and outline their applications as new drug delivery systems or supramolecular toolboxes containing, for example, enzymes capable of converting nontoxic prodrugs into toxic drugs at a designated location. Such functionalized nanocontainers offer a wide range of applications including enzymatic catalysis, controlled release, and directed drug delivery in medicine due to their multifunctionality. The unique advantage of capsules in comparison to other systems is that they can be functionalized or loaded simultaneously with the above‐mentioned components, thus permitting multifunctional processes in single cells.