Diatom microalgae are a natural source of fossil biosilica shells, namely the diatomaceous earth (DE), abundantly available at low cost. High surface area, mesoporosity and biocompatibility, as well as the availability of a variety of approaches for surface chemical modification, make DE highly profitable as a nanostructured material for drug delivery applications. Despite this, the studies reported so far in the literature are generally limited to the development of biohybrid systems for drug delivery by oral or parenteral administration. Here we demonstrate the suitability of diatomaceous earth properly functionalized on the surface with -octyl chains as an efficient system for local drug delivery to skin tissues. Naproxen was selected as a non-steroidal anti-inflammatory model drug for experiments performed both in vitro by immersion of the drug-loaded DE in an artificial sweat solution and, for the first time, by trans-epidermal drug permeation through a 3D-organotypic tissue that better mimics the in vivo permeation mechanism of drugs in human skin tissues. Octyl chains were demonstrated to both favour the DE adhesion onto porcine skin tissues and to control the gradual release and the trans-epidermal permeation of Naproxen within 24 h of the beginning of experiments. The evidence of the viability of human epithelial cells after permeation of the drug released from diatomaceous earth, also confirmed the biocompatibility with human skin of both Naproxen and mesoporous biosilica from diatom microalgae, disclosing promising applications of these drug-delivery systems for therapies of skin diseases.