Accurate temperature measurements with a high spatial resolution for application in the biomedical fields demand novel nanosized thermometers with new advanced properties. Here, a water dispersible ratiometric temperature sensor is fabricated by encapsulating in silica nanoparticles, organic capped PbS@CdS@CdS “giant” quantum dots (GQDs), characterized by dual emission in the visible and near infrared spectral range, already assessed as efficient fluorescent nanothermometers. The chemical stability, easy surface functionalization, limited toxicity and transparency of the silica coating represent advantageous features for the realization of a nanoscale heterostructure suitable for temperature sensing. However, the strong dependence of the optical properties on the morphology of the final core–shell nanoparticle requires an accurate control of the encapsulation process. We carried out a systematic investigation of the synthetic conditions to achieve, by the microemulsion method, uniform and single core silica coated GQD (GQD@SiO2) nanoparticles and subsequently recorded temperature-dependent fluorescent spectra in the 281-313 K temperature range, suited for biological systems. The ratiometric response—the ratio between the two integrated PbS and CdS emission bands—is found to monotonically decrease with the temperature, showing a sensitivity comparable to bare GQDs, and thus confirming the effectiveness of the functionalization strategy and the potential of GQD@SiO2 in future biomedical applications.