We suggest a new strategy for creating stimuli-responsive bio-integrated optical nanostructures based on Mie-resonant silicon nanoparticles covered by an ensemble of similarity negatively charged polyelectrolytes (heparin and sodium polystyrene sulfonate). The dynamic tuning of the nanostructures’ optical response is due to light-induced heating of the nanoparticles and swelling of the polyelectrolyte shell. The resulting hydrophilic/hydrophobic transitions significantly change the shell thickness and reversible shift of the scattering spectra for individual nanoparticles up to 60 nm. Our findings bring novel opportunities for the application of smart nanomaterials in nanomedicine and bio-integrated nanophotonics.