Intravital fluorescence imaging has great potential in biological and biomedical research, as it provides the ability to directly observe biological structures and processes in their natural state. Contrast agents for intravital imaging applications should exhibit good biocompatibility, multiphoton fluorescence, and long emission. Carbon nanodots and semiconductor nanocrystals meet these requirements in most cases, with the added benefit that their properties can be 'tuned' for specific applications by controlling the size and surface chemistry of the nanoparticles. Here, we report on a simple heat-assisted strategy to fabricate SiOx-core self-assembled nanodots using self-assembled monolayer (SAM) materials. Our results demonstrate that substrate-free self-assembled nanodots from alkylalkoxysilane exhibit controllable structural and chemical characteristics that are well suited for applications in biological, biomedical, and clinical research, and may find further use in optoelectronic and sensor devices.