The investigation of solid speciation of metals and metalloids is required for accurate assessment of the hazardous properties of solid waste materials from high-temperature technologies (slag, bottom ash, fly ash, air-pollution-control residues). This paper deals with the problem of reliability of microanalyses using a combination of electron microprobe analysis (EPMA) and scanning electron microscopy (SEM) only. These methods do not permit to detect nanophases in host-crystals and lead to erroneous interpretation of analytical results, considering the elements of nanophases as belonging to the crystal structure of the main phase. More detailed analysis using transmission electron microscopy (TEM) on foils prepared by focused ion beam (FIB) can be used to solve this analytical problem. In this study, lamellar aggregates of potassium-rich clinopyroxenes were detected in copper smelting slags by a combination of SEM and EPMA. However, FIB-TEM indicated the presence of leucite inclusions (tens to hundreds nm in size) within the clinopyroxene lamellae. Based on examples from smelting slags and other solid waste materials, recommendations for standard SEM and EPMA applications and the need for methods with higher resolution for mineralogical investigation of waste materials are discussed.