Owing to the ubiquitous availability and simple biocatalysis, the anti-proliferative laccase holds enormous opportunities for anti-cancer applications. However, accessing efficient and specific (super-magnetically targetable) new delivery system for anti-proliferative laccase is vital step towards laccase based anti-cancer approach. Therefore, in this investigation, super-magnetized (Fe3O4) and chitosan (CS) functionalized halloysite nanotubes (HNTs) (termed as Fe3O4-HNTs-CS) was facile synthesized. Further, laccase from Trametes versicolor was immobilized on Fe3O4-HNTs-CS (termed as Fe3O4-HNTs-CS-Lac). Then free laccase and Fe3O4-HNTs-CS-Lac were evaluated for anti-proliferative properties against cancer cell lines of liver (HepG2), lung (H460), cervix (Hela) and stomach (AGS). Laccase and Fe3O4-HNTs-CS-Lac gave significant cytotoxicity against all studied cancer cell lines. Moreover, the apoptosis analysis and FE-SEM morphology observations of cells support the anti-proliferative potential of laccase immobilized on Fe3O4-HNTs-CS. Therefore, investigated Fe3O4-HNTs-CS-Lac is natural and super-magnetic nano-biocatalyst, having the significant anti-proliferative potential and furthermore, Fe3O4-HNTs-CS can be used as efficient and specific delivery system for other anti-cancer enzymes.