Currently, highly demanded biodegradable or bio-sourced plastics exhibit inherent drawbacks due to their limited processability and end-use properties (barrier, mechanical, etc.). To overcome all of these shortcomings, the incorporation of lamellar inorganic particles, such as layered double hydroxides (LDH) seems to be appropriate. However, LDH delamination and homogenous dispersion in a polymer matrix without use of harmful solvents, remains a challenging issue, which explains why LDH-based polymer nanocomposites have not been scaled-up yet. In this work, LDH with intercalated ionic liquid (IL) anions were synthesized by a direct co-precipitation method in the presence of phosphonium IL and subsequently used as functional nanofillers for in-situ preparation of poly (butylene adipate-co-terephthalate) (PBAT) nanocomposites. The intercalated IL-anions promoted LDH swelling in monomers and LDH delamination during the course of in-situ polycondensation, which led to the production of PBAT/LDH nanocomposites with intercalated and exfoliated morphology containing well-dispersed LDH nanoplatelets. The prepared nanocomposite films showed improved water vapor permeability and mechanical properties and slightly increased crystallization degree and therefore can be considered excellent candidates for food packaging applications.