Chitin nanofibrils (CN) and nanolignin (NL) were used to embed active molecules, such as vitamin E, sodium ascorbyl phosphate, lutein, nicotinamide and glycyrrhetinic acid (derived from licorice), in the design of antimicrobial, anti-inflammatory and antioxidant nanostructured chitin nanofibrils–nanolignin (CN-NL) complexes for skin contact products, thus forming CN-NL/M complexes, where M indicates the embedded functional molecule. Nano-silver was also embedded in CN-NL complexes or on chitin nanofibrils to exploit its well-known antimicrobial activity. A powdery product suitable for application was finally obtained by spray-drying the complexes co-formulated with poly(ethylene glycol). The structure and morphology of the complexes was studied using infrared spectroscopy and field emission scanning electron microscopy, while their thermal stability was investigated via thermo-gravimetry. The latter provided criteria for evaluating the suitability of the obtained complexes for subsequent demanding industrial processing, such as, for instance, incorporation into bio-based thermoplastic polymers through conventional melt extrusion. In vitro tests were carried out at different concentrations to assess skin compatibility. The obtained results provided a physical–chemical, morphological and cytocompatibility knowledge platform for the correct selection and further development of such nanomaterials, allowing them to be applied in different products. In particular, chitin nanofibrils and the CN-NL complex containing glycyrrhetinic acid can combine excellent thermal stability and skin compatibility to provide a nanostructured system potentially suitable for industrial applications.