Microporous materials can provide interesting tools for different goals from bioimaging to the delivery of bioactive molecules. In this study, the procedure based on cryo-approaches was designed to formulate the nanoparticles of natural clinoptilolite from the Zeolites mineral family. Applying scanning electron microscopy, clinoptilolite samples were imaged. After aging in the ethanol solution of phosphatidylcholine (lecithin), nanoparticles were encapsulated in the lecithin envelope. The adsorption of lecithin by clinoptilolite nanoparticles was studied by registering the diminution of optical density (OD 235) for ethanol/lecithin solution at 235 nm with UV spectrometry. The kinetics of lecithin/clinoptilolite complex development was shown to exhibit intricate behavior, when the adsorption of lecithin was followed with its gradual release resulting in the increase of lecithin content in ethanol solution back toward the original level. The size distribution for the lecithin/clinoptilolite complex was determined with a dynamic light scattering technique. To our knowledge, there are no reports of natural clinoptilolite-based platforms that were used as the for a nanosized capsule with phospholipids shell.