Energy dispersive X-ray spectrometry (EDS) is a powerful tool for research studies on building materials. Elemental quantification in cementitious phases contained in the concrete microstructure can be performed at an excellent spatial resolution. However, accurate compositional quantification requires a standard-based analysis, whereas currently the most common are standardless microanalysis. Reasons behind this approach lie on the difficulty of finding appropriate microanalysis standards in EDS studies. In standard-less analyses, elemental quantification from an EDS spectrum provides normalized quantification, i.e. an analytical total of 100%. Most EDS detectors cannot provide reliable data for elements with smaller atomic number than sodium, which results in the stoichiometric determination of oxygen. The aim of this paper is raise awareness about the importance of a controlled experimental parameters and the use of mineral standards when performing EDS analysis on cementitious materials. For this purpose, both types of investigation (with and without standards) are performed simultaneously in order to obtain chloride profiles in six reinforced mortar specimens subjected to chloride ingress and carbonation. Results illustrate that differences in element concentrations can be derived by the absence of mineral standards which could lead to inaccurate interpretations of element concentrations such as chlorine.