A novel bio-hybrid drug delivery system was obtained involving a Mg/Al-NO3 layered double hydroxide (LDH) intercalated either with ibuprofenate anions (IBU) or a phospholipid bilayer (BL) containing a neutral drug, i.e., 17β-estradiol, and then embedded in chitosan beads. The combination of these components in a hierarchical structure led to synergistic effects investigated through characterization of the intermediates and the final bio-composites by XRD, TG, SEM, and TEM. That allowed determining the presence and yield of IBU and of BL in the interlayer space of LDH, and of the encapsulated LDH in the beads, as well as the morphology of the latter. Peculiar attention has been paid to the intercalation process of the BL for which all available data substantiate the hypothesis of a first interaction at the defect of the LDH, as well as on the interaction mode of these components. 1H, 31P and 27Al MAS-NMR studies allowed establishing that the intercalated BL is not homogeneous and likely formed patches. Release kinetics were performed for sodium ibuprofenate as well as for the association of 17β-estradiol within the negatively charged BL, each encapsulated in the LDH/chitosan hybrid materials. Such new bio-hybrids offer an interesting outlook into the pharmaceutical domain with the ability to be used as sustained release systems for a wide variety of anionic and, importantly, neutral drugs.