This work demonstrates the capabilities of nanoscale secondary-ion mass spectrometry, using the Cameca NanoSIMS50 ion microprobe, to detect and image the copper-ion distribution in microalgal cells exposed to nanomolar and micromolar copper concentrations. In parallel to 63Cu− secondary-ion maps, images of 12C−,12C14N−, and 31P− secondary ions were collected and analysed. A correlation of 63Cu− secondary-ion maps with those found for 12C14N− and 31P− demonstrated the possible association of Cu with cell components rich in proteins and phosphorus. The results highlighted the potential of Nano- SIMS for intracellular tracking of essential trace elements such as Cu in single cells of the microalga Chlorella kesslerii.