Pyrrolizidine alkaloids are plant secondary metabolites that have recently attracted attention as toxic contaminants in various foods and feeds as they are often harvested by accident. Furthermore, they prove themselves as hard to analyze due to their wide structural range and low concentration levels. However, even low concentrations show toxic behavior in the form of chronic liver diseases and possible carcinogenicity. Since sample preparation for this compound group is in need of more green and sustainable alternatives, modified halloysite nanotubes present an interesting approach. Based on the successful use of sulfonated halloysite nanotubes as inexpensive, easy-to-produce cation exchangers for solid phase extraction in our last work, this study deals with the further modification of the raw nanotubes and their performance in the solid phase extraction of pyrrolizidine alkaloids. Conducting already published syntheses of two organosilyl-sulfonated halloysite nanotubes, namely HNT-PhSO3H and HNT-MPTMS-SO3H, both materials were used as novel materials in solid phase extraction. After the optimization of the extraction protocol, extractions of aqueous pyrrolizidine alkaloid mixtures showed promising results with recoveries ranging from 78.3% to 101.3%. Therefore, spiked honey samples were extracted with an adjusted protocol. The mercaptopropyl-sulfonated halloysite nanotubes revealed satisfying loading efficiencies and recoveries. Validation was then performed, which displayed acceptable performance for the presented method. In addition, reusability studies using HNT-MPTMS-SO3H for solid phase extraction of an aqueous pyrrolizidine alkaloid mixture demonstrated excellent results over six cycles with no trend of recovery reduction or material depletion. Therefore, organosilyl-sulfonated halloysite nanotubes display a green, efficient and low-cost alternative to polymeric support in solid phase extraction of toxic pyrrolizidine alkaloids from complex honey matrix.