Nanoparticle uptake by cells is a key parameter in their performance in biomedical applications. However, the use of quantitative, non-destructive techniques to obtain the amount of nanoparticles internalized by cells is still uncommon. We have studied the cellular uptake and the toxicity of core-shell maghemite-silica magnetic nanoparticles (MNPs), with a core diameter of 9 nm and a shell thickness of 3 nm. The internalization of the nanoparticles by mouse neuroblastoma 2a cells was evaluated by sensitive and non-destructive Superconducting Quantum Interference Device (SQUID) magnetometry and corroborated by graphite furnace atomic absorption spectroscopy. We were thus able to study the toxicity of the nanoparticles for well-quantified MNP uptake in terms of nanoparticle density within the cell. No significant variation in cell viability or growth rate was detected for any tested exposure. Yet, an increase in both the amount of mitochondrial superoxide and in the lysosomal activity was detected for the highest concentration (100 μg ml
−1
) and incubation time (24 h), suggesting the onset of a disruption in ROS homeostasis, which may lead to an impairment in antioxidant responses. Our results validate SQUID magnetometry as a sensitive technique to quantify MNP uptake and demonstrate the non-toxic nature of these core-shell MNPs under our culture conditions.