The properties of the environment, such as pH, ionic composition, relative permittivity, or molecular crowding effect, sensitively modulate the biomolecular structures and interactions. Understandably, the characterization of biomolecules should be performed under physiologically relevant conditions. The in-cell NMR spectroscopy is a high-resolution approach allowing the characterization of biomolecular structure and interactions in the complex intracellular space of living cells. Thus far, in-cell NMR spectroscopy has remained limited to asynchronous 2D cultures of mammalian (human) cells. However, the intracellular environment is not constant throughout the cell's life: It changes during the cell cycle, as the cell undergoes apoptosis, or when exposed to external stress. Here, we show adaptations of the in-cell NMR method that allow studying the structure of biomolecules at defined physiological states of the cell. Moreover, we extend the in-cell NMR measurements from the cell suspension to 3D spheroid, a cell biology model of tissue accounting for intercellular communication.