Polymeric anthocyanins are biologically active, pH-sensitive natural compounds and pigments with beneficial functional, pharmacological and therapeutic properties for consumer health. More recently, they have been used for the manufacture of active and pH-sensitive (“intelligent”) food nanopackaging, due to their bathochromic effect. Nevertheless, in order for polymeric anthocyanins to be included either as a functional food or as a pharmacological additive (medicinal food), they inevitably need to be stabilized, as they are highly susceptible to environmental conditions. In this regard, nanopackaging has become a tool to overcome the limitations of polymeric anthocyanins. The objective of this study was to evaluate their structural, thermal, morphological, physicochemical, antioxidant and antimicrobial properties, as well as their responses to pH changes, and the cytotoxicity of blends made from polymeric anthocyanins extracted from Jamaica flowers (Hibiscus sabdariffa) and natural or organo-modified montmorillonite (Mt), as active and pH-sensitive nanopackaging. This study allowed us to conclude that organo-modified Mts are efficient pH-sensitive and antioxidant nanopackaging systems that contain and stabilize polymeric anthocyanins compared to natural Mt nanopackaging and stabilizing polymeric anthocyanins. However, the use of these polymeric anthocyanin-stabilizing organo-modified Mt-based nanopackaging systems are limited for food applications by their toxicity.