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This study examines carboxymethyl chitosan-based microcapsules created by spray drying as a method for delivering biologically active compounds isolated from the <jats:italic>Cistus<\/jats:italic> herb. Effects of sterilization and encapsulation on the polyphenol and flavonoid content of <jats:italic>Cistus<\/jats:italic> extract were investigated to optimize the production process. Furthermore, <jats:italic>in vitro<\/jats:italic> studies were carried out to examine the anticancer properties of sterilized polyphenols and flavonoids on glioblastoma cells isolated from oncological patients. Acquired results show high anticancer potential towards glioblastoma as well as low cytotoxicity towards non-cancer cell lines by the substances in question. Steam sterilization is shown to affect the content of biologically active compounds the least. 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