This paper presents an investigation of the limitations and optimisation of energy dispersive X-ray (EDX) tomography within the scanning transmission electron microscope, focussing on application of the technique to characterising the 3D elemental distribution of bimetallic AgAu nanoparticles. The detector collection efficiency when using a standard tomography holder is characterised using a tomographic data set from a single nanoparticle and compared to a standard low background double tilt holder. Optical depth profiling is used to investigate the angles and origin of detector shadowing as a function of specimen field of view. A novel time-varied acquisition scheme is described to compensate for variations in the intensity of spectrum images at each sample tilt. Finally, the ability of EDX spectrum images to satisfy the projection requirement for nanoparticle samples is discussed, with consideration of the effect of absorption and shadowing variations. •We investigate the methodology of STEM-EDX tomography of nanoparticles.•We present a time-varied acquisition scheme to compensate for detector shadowing.•The ability of STEM-EDX tomography to meet the projection requirement is discussed.