This work proposes a new strategy for the immobilization of semiconductor nanocrystals by carrying out in simultaneous the synthesis of silica nanostructures and the encapsulation of MPA-capped CdTe quantum dots (QDs). The developed approach was bioinspired on the nature occurring biosilicification process that some organisms, like diatoms and sponges, use to produce nanostructures of silica, and prevents the use of harsh and environmentally unfriendly conditions such as toxic and expensive organic solvents, high temperature and pressure and extreme pH values. Different parameters that could influence the silica particle synthesis and the QD immobilization, such as silica precursors, catalysts and ions concentration, pH and amount of QDs were evaluated. Encapsulation efficiency, size and the shape of biosilica structures were also determined by the experimental conditions. Immobilization and QDs concentration has a strong impact on QDs fluorescence and on the silica-QDs nanostructures stability.