Abstract We present a tomography technique which couples scanning transmission electron microscopy (STEM) and X-ray energy dispersive spectrometry (XEDS) to resolve 3D distribution of elements in nanoscale materials. STEM imaging when combined with XEDS mapping using a symmetrically arranged XEDS detector design around the specimen overcomes many of the obstacles in 3D chemical imaging of nanoscale materials and successfully elucidates the 3D chemical information in a large field of view of the transmission electron microscopy (TEM) sample. We employed this technique to investigate 3D distribution of Nickel (Ni), Manganese (Mn) and Oxygen (O) in a Li1.2Ni0.2Mn0.6O2 (LNMO) nanoparticle used as a cathode material in Lithium (Li) ion batteries. For this purpose, 2D elemental maps were acquired for a range of tilt angles and reconstructed to obtain 3D elemental distribution in an isolated LNMO nanoparticle. The results highlight the strength of this technique in 3D chemical analysis of nanoscale materials by successfully resolving Ni, Mn and O elemental distributions in 3D and discovering the new phenomenon of Ni surface segregation in this material. Furthermore, the comparison of simultaneously acquired high angle annular dark field (HAADF) STEM and XEDS STEM tomography results shows that XEDS STEM tomography provides additional 3D chemical information of the material especially when there is low atomic number (Z) contrast in the material of interest.