Metal complexes are emerging as promising alternatives to traditional platinum-based cancer treatments, offering reduced side effects. However, understanding their cellular uptake and distribution and quantify their presence at the single cell level remains challenging. Advanced imaging techniques, including transmission electron microscopy (TEM), synchrotron radiation X-ray fluorescence (SR-XRF) and energetic ion beam-based nuclear microscopy (STIM, scanning transmission ion microscopy; PIXE, particle-induced X-ray emission; EBS, elastic backscattering spectrometry), allow detailed high-resolution visualization of structure and morphology, high sensitivity for elemental detection with quantification within single cells, and the construction of three-dimensional (3D) models of metal distribution, positioning them as powerful tools for assessing the cellular uptake and compartmentalisation of complexes. Three Cu(II) complexes [Cu(phen)2(H2O)](NO3)2 (1), [Cu(Me2phen)2(NO3)]NO3 (2) and [Cu(amphen)2(H2O)](NO3)2 (3), (phen = 1,10-phenanthroline, Me2phen = 4,7-dimethyl-1,10-phen, amphen = 5-amino-phen) were investigated for Cu uptake and distribution in PC3 prostate cancer cells. All complexes show significant Cu-uptake regardless of media concentration. Cu-concentrations in cytoplasm and nucleus are similar between treatments. Complexes 1 and 3 concentrate Cu in the nuclear region and show a vesicle-like pattern around the nucleus, while 2 shows a dispersed cytoplasmic pattern with large vesicles. The 3D models confirm that Cu is not retained at the plasma membrane, with complex 1 targeting the nucleus and 2 remaining in the cytoplasm. These results highlight the importance of quantifying metal distribution and correlating it with structural changes to understand the relevance of the ligand in the mechanisms of cellular uptake and targeting, crucial for the development of effective metal-based cancer therapies.