Biopolymers, which are biodegradable and inherently functional, have high potential for specialized applications (e.g., disposable and transient systems and biomedical treatment). For this, it is important to create composite materials with precisely defined chain interactions and tailored properties. This work shows that for a chitosan–gelatin material, both glycerol and isosorbide are effective plasticizers, but isosorbide could additionally disrupt the polyelectrolyte complexation (PEC) between the two biopolymers, which greatly impacts the glass transition temperature (Tg), mechanical properties, and water absorption. While glycerol-plasticized samples without nanofiller or with graphene oxide (GO) showed minimal water uptake, the addition of isosorbide and/or montmorillonite (MMT) made the materials hydrolytically unstable, likely due to disrupted PEC. However, these samples showed an opposite trend in surface hydrophilicity, which means surface chemistry is controlled differently from chain structure. This work highlights different mechanisms that control the different properties of dual-biopolymer systems and provides an updated definition of biopolymer plasticization, and thus could provide important knowledge for the future design of biopolymer composite materials with tailored surface hydrophilicity, overall hygroscopicity, and mechanical properties that meet specific application needs.