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The use of fluorescence microscopy to study fate and transport of nanoparticles in the environment can be limited by the presence of confounding background signals such as autofluorescence and scattered light. The unique spin-related luminescence properties of nitrogen vacancy (NV) centers in diamond nanoparticles (NVND) enable new types of imaging modalities such as selective imaging of nanoparticles in the presence of background fluorescence. These techniques make use of the fact that the spin properties, which affect the fluorescence of NV centers, can be modulated using applied magnetic or radio-frequency fields. This work presents the use magnetic fields to modulate the fluorescence of NVND for background-subtracted imaging of nanoparticles ingested by a model organism, C. elegans . With the addition of modest time-modulated magnetic fields from an inexpensive “hobby” electromagnet, the fluorescence of 40 nm NVND can be modulated by 10% in a widefield imaging configuration. Herein, differential magnetic imaging is used to image and to isolate the fluorescence arising from nanodiamond within the gut of the organism C. elegans . This method represents a promising approach to probing the uptake of nanoparticles by organisms and to assessing the movement and interactions of nanoparticles in biological systems.