This work describes the effects of different plasticizers, namely, glycerol, triacetin, and 1-ethyl-3-methylimidazolium acetate ([C2 mim][OAc]), on the structure and properties of thermomechanically processed, bulk chitosan and chitosan/alginate materials. Mechanical data shows that, for the chitosan matrix, glycerol and [C2 mim][OAc] were highly effective at reducing intra- and intermolecular forces between biopolymer chains, leading to increased ductility, while the plasticization effect of triacetin was minor. Nonetheless, this triester effectively suppressed biopolymer recrystallization, whereas [C2 mim][OAc] promoted it. In contrast, for the chitosan/alginate matrix, inclusion of triacetin resulted in increased recrystallization, higher thermal stability, and excellent mechanical properties. The triacetin assisted the interactions between biopolymer chains in this polyelectrolyte complexed system. In contrast, the chitosan/alginate material plasticized by [C2 mim][OAc] displayed the most apparent phase separation, poorest mechanical properties, and highest surface hydrophilicity, behavior associated with the disruption of polyelectrolyte complexation and hydrogen bonding between biopolymer chains. Interestingly, the formation of a "new structure" under the electron beam during microscopy imaging was observed, likely from coordination between alginate and [C2 mim][OAc]. Thus, this work has revealed the strong and unexpected effects of three different plasticizers on the hydrogen bonding and electrostatic interactions within chitosan/alginate polyelectrolyte complexed materials, which have potential for biomedical applications where balanced hydrophilicity and mechanical properties are required.