Cultivation of the fungal species Aspergillus parasiticus led to the isolation of Kojic acid (KA), an important secondary metabolite, but unstable under some conditions. In order to improve the pharmacokinetic potential of KA for biotechnological applications in pharmaceutical and cosmetic formulations, KA was immobilized in mesoporous nanomaterials based on silica (MSN). This kind of inorganic support has been intensively studied as candidates for controlling-release drugs, due to its high surface area, high ordering of mesopores and pore size in nanometer scale. In this way, mesoporous silica nanoparticles have been synthesized and were chemically modified by post-synthesis with 3-aminopropyltriethoxysilane (MSNAPTES) and the influence of functionalization of the matrix on the loading rate of KA was studied. Nanoparticles were physicochemical characterized by SAXS, SEM, CHN, TGA, N2 adsorption, photon correlation spectroscopy and zeta potential analysis. Bactericidal efficacy of these nanoparticles was tested against different microorganisms, and these new kojic acid nanoparticles showed high bactericidal efficiency. In relation to acetylcholinesterase (AChE) inhibition test, used to screen drugs active to treat Alzheimer’s disease patients, MSNAPTES KA nanoparticles showed to be as efficient as the free-acid. KA loading showed also tyrosine inhibitory property preserved. The results points that, although free-kojic acid amount in MSNAPTES KA is thirty times lower, biological activity of this nanoparticle is as high as the activity of free-kojic acid, being, therefore, a highly and multi-active nano-system for kojic acid delivery with improved pharmacokinetic skills and a wide scope of industrial applications.