Despite efforts in producing nanoparticles with tightly controlled designs and specific physicochemical properties, these can undergo massive nano−bio interactions and bioprocessing upon internalization into cells. These transformations can generate adverse biological outcomes and premature loss of functional efficacy. Hence, understanding the intracellular fate of nanoparticles is a necessary prerequisite for their introduction in medicine. Among nanomaterials devoted to theranostics are copper sulfide (CuS), which provides outstanding optical properties along with easy synthesis and low cost. Herein, we performed a long-term multiscale study on the bioprocessing of hollow CuS nanoparticles (CuS NPs) and rattle-like iron oxide nanoflowers@ CuS core−shell hybrids (IONF@CuS NPs) when inside stem cells and cancer cells, cultured as spheroids. In the spheroids, both CuS NPs and IONF@CuS NPs are rapidly dismantled into smaller units (day 0 to 3), and hair-like nanostructures are generated (days 9−21). This bioprocessing triggers an adaptation of the cellular metabolism to the internalized metals without impacting cell viability, differentiation, or oxidative stress response. Throughout the remodeling, a loss of IONF-derived magnetism is observed, but, surprisingly, the CuS photothermal potential is preserved, as demonstrated by a full characterization of the photothermal conversion across the bioprocessing process. The maintained photothermal efficiency correlated well with synchrotron X-ray absorption spectroscopy measurements, evidencing a similar chemical phase for Cu but not for Fe over time. These findings evidence that the intracellular bioprocessing of CuS nanoparticles can reshape them into bioengineered nanostructures without reducing the photothermal function and therapeutic potential.