As, in the market, poly (lactic acid) (PLA) is the most used polymer as an alternative to conventional plastics, and as functionalized chitin nanocrystals (CHNC) can provide structural and bioactive properties, their combination sounds promising in the preparation of functional nanocomposite films for sustainable packaging. Chitin nanocrystals were successfully modified via acylation using anhydride acetic and dodecanoyl chloride acid to improve their compatibility with the matrix, PLA. The nanocomposite films were prepared by extrusion/compression approach using different concentrations of both sets of functionalized CHNC. This investigation brings forward that both sets of modified CHNC act as functional agents, i.e., they slightly improved the hydrophobic character of the PLA nanocomposite films, and, very importantly, they also enhanced their antifungal activity. Nonetheless, the nanocomposite films prepared with the CHNC modified with dodecanoyl chloride acid presented the best properties.