Traditional electron microscopy (EM) can be complemented with analytical EM to increase objective sample information enabling feature identification. Energy dispersive X-ray (EDX) imaging provides semi-quantitative elemental composition of the sample with high spatial resolution (~10nm) in ultrathin sections. However, EDX imaging of biological samples is still challenging as a routine method because many elements are at the detection limit for this technique. Moreover, samples undergo extensive preparation before analysis, which can introduce disruptive X-ray cross-talk or artifacts. EDX data can, for instance, be skewed by (i) osmium interference with endogenous phosphorus, (ii) chlorine present in EPON-embedded tissues, (iii) lead interference with endogenous sulfur, and (iv) potential spectral overlaps with grid material, contrast agents, and the in-microscope sample holder. Here, we highlight how to circumvent these potential pitfalls and outline how we approach sample preparation and analysis for detection of different elements of interest. Utilization of well-considered a priori sample preparation techniques will best ensure conclusive EDX experiments.