The functionalization of nanoporous zeolite L crystals with β-cyclodextrin (CD) has been demonstrated. The zeolite surface was first modified with amino groups by using two different aminoalkoxysilanes. Then, 1,4-phenylene diisothiocyanate was reacted with the amino monolayer and used to bind CD heptamine by using its remaining isothiocyanate groups. The use of the different aminoalkoxysilanes, 3-aminopropyl dimethylethoxysilane (APDMES) and 3-aminopropyl triethoxysilane (APTES), led to drastic differences in uptake and release properties. Thionine was found to be absorbed and released from amino- and CD-functionalized zeolites when APDMES was used, whereas functionalization by APTES led to complete blockage of the zeolite channels. Fluorescence microscopy showed that the CD groups covalently attached to the zeolite crystals could bind adamantyl-modified dyes in a specific and reversible manner. This strategy allowed the specific immobilization of His-tagged proteins by using combined host–guest and His-tag-Ni-nitrilotriacetic acid (NTA) coordination chemistry. Such multifunctional systems have the potential for encapsulation of drug molecules inside the zeolite pores and non-covalent attachment of other (for example, targeting) ligand molecules on its surface.