Biopolymer-based drug delivery systems have gained considerable attention in the field of nanomedicine. In this study, a protein-polysaccharide conjugate was synthesized by covalent conjugation of the enzyme horseradish peroxidase (HRP) with acetalated dextran (AcDex) via a thiol exchange reaction. The resulting bioconjugate shows a dual-responsive behavior in acidic and reductive environments to achieve a controlled release of drugs. The self-assembly of this amphiphilic HRP-AcDex conjugate allows the encapsulation of prodrug indole-3-acetic acid (IAA) into the hydrophobic polysaccharide core. Under slightly acidic conditions, the acetalated polysaccharide reverts to its native hydrophilic form, which triggers the disassembly of micellar nanoparticles and the release of the encapsulated prodrug. The conjugated HRP further activates the prodrug by oxidation of IAA into cytotoxic radicals, which leads to cellular apoptosis. The results indicate that the HRP-AcDex conjugate in combination with IAA has great potential to be used as a novel enzyme prodrug therapy for cancer treatment.