In this study, we have developed innovative polymer nanocomposites by integrating magnesium-aluminum layered double hydroxide (LDH)-based nanocarriers modified with functional molecules into a fully biobased poly(lactic acid)/poly(butylene succinate-co-adipate) (PLA/PBSA) matrix. These LDH-based hybrid host-guest systems contain bioactive compounds like rosmarinic acid, ferulic acid, and glycyrrhetinic acid, known for their antioxidant, antimicrobial, and anti-inflammatory properties. The bioactive molecules can be gradually released from the nanocarriers over time, allowing for sustained and controlled delivery in various applications, such as active packaging or cosmetics. The morphological analysis of the polymer composites, prepared using a discontinuous mechanical mixer, revealed the presence of macroaggregates and nano-lamellae at the polymer interface. This resulted in an enhanced water vapor permeability compared to the original blend. Furthermore, the migration kinetics of active molecules from the thin films confirmed a controlled release mechanism based on their immobilization within the lamellar system. Scaling-up experiments evaluated the materials’ morphology and mechanical and thermal properties. Remarkably, stretching deformation and a higher shear rate during the mixing process enhanced the dispersion and distribution of the nanocarriers, as confirmed by the favorable mechanical properties of the materials.