We used hyperspectral-enhanced dark field microscopy for studying physicochemical changes in biomaterials by tracking their unique spectral signatures along their pathway through different biological environments typically found in any biomedical application. We correlate these spectral signatures with discrete environmental features causing changes in nanoparticles’ physicochemical properties. We use this correlation to track the nanoparticles intracellularly and to assess the impact of these changes on their functionality. We focus on one example of a photothermal nanocomposite, i.e., polymer-coated gold/copper sulfide nanoparticles, because their performance depends on their localized surface plasmon peak, which is highly sensitive to environmental changes. We found spectral differences both in the dependence of time and discrete environmental factors, affecting the range of illumination wavelengths that can be used to activate the functionality of these types of nanoparticles. The presence of proteins (protein corona) and the increase in ionic strength induce a spectral broadening towards the NIR region which we associated with nanoparticles’ agglomeration. In acidic environments, such as that of the lysosome, a red shift was also observed in addition to a decrease in the scattering intensity probably associated with a destabilization of the proteins and/or the change in the net charge of the polymer around the nanoparticles. We observed a loss of the photo-excitation potential of those nanoparticles exposed to acidic conditions in the <600 nm spectral rage. In a similar manner, ageing induces a transitioning from a broad multipeak spectrum to a distinct shoulder with time (up to 8 months) with the loss of spectral contribution in the 450–600 nm range. Hence, a fresh preparation of nanoparticles before their application would be recommended for an optimal performance. We highlight the impact of ageing and the acidic environment on the responsiveness of this type of plasmonic nanoparticle. Regardless of the spectral differences found, polymer-coated gold/copper sulfide nanoparticles retained their photothermal response as demonstrated in vitro upon two-photon irradiation. This could be ascribed to their robust geometry provided by the polymer coating. These results should be useful to rationally design plasmonic photothermal probes.