Diatoms are a large group of single-celled, eukaryotic microalgae that are found throughout the world’s oceans and freshwater habitats. The characteristic feature of each diatom is a silica-based cell wall that exhibits a unique architecture with species-specific micro-and nanopatterns. Here we describe a method that enables the immobilization of functional proteins (GFP, enzyme HabB) in the silica matrix of the diatom Thalassiosira pseudonana in vivo. The method is based on genetic engineering of the organism’s silica forming machinery, and represents a paradigm for utilizing biominerals for the biotechnological production of nanopatterned materials with tailored functionalities. Such materials are attractive for sensor applications (e.g. biosensors, microarrays, microfluidic devices), as reusable biocatalysts for organic syntheses and degradation of harmful chemicals (remediation), and for drug delivery.