The use of magnetic nanoparticles in nanomedicine keeps expanding and, for most applications, the nanoparticles are internalized in cells then left within, bringing the need for accurate, fast, and easy to handle methodologies to assess their behavior in the cellular environment. Herein, a benchtop-size magnetic sensor is introduced to provide real-time precise measurement of nanoparticle magnetism within living cells. The values obtained with the sensor, of cells loaded with different doses of magnetic nanoparticles, are first compared to conventional vibrating sample magnetometry (VSM), and a strong correlation remarkably validates the use of the magnetic sensor as magnetometer to determine the nanoparticle cellular uptake. The sensor is then used to monitor the progressive intracellular degradation of the nanoparticles, over days. Importantly, this real-time in situ measure is performed on a stem cell-spheroid tissue model and can run continuously on a same spheroid, with cells kept alive within. Besides, such continuous magnetic measurement of cell magnetism at the tissue scale does not impact either tissue formation, viability, or stem cell function, including differentiation and extracellular matrix production.