This article presents in detail the methodology dedicated strictly to loess mineralogical investigation by automated mineralogy system QEMSCAN® (quantitative evaluation of minerals by scanning electron microscopy (SEM)), which couples SEM and energy dispersive X-ray spectrometry to automatically deliver mineral and phase mapping. The present study provides guidelines for further loess investigation in Poland, in order to maintain the complete comparability of results which will be obtained. The methodology is then used to obtain the data on complex mineralogical composition (heavy, light, transparent and opaque phases). In total 1,159,107 particles have been measured for five bulk loess samples and 4–6% of them were heavy minerals (c.a. 10,000 per sample). The bulk samples are dominated by quartz (57.3–62.9%) and contain plagioclase (7.8–9.2%), K-feldspar (7.9–8.7%), carbonates (5.0–7.8%), muscovite (3.2–6.2%), biotite (4.2–7.5%), heavy minerals (4.3–5.8%) and clay minerals (0.9–1.6%). The heavy minerals (as a group recalculated to 100%) are mainly represented by phases such as clinopyroxene (38–51%), garnets (14–21%), TiO2 polymorphs (8–12%), Al2SiO5 polymorphs (3–7%), ilmenite (3–6%), iron oxides, e.g., hematite and magnetite (2–5%) and zircon (∼2%). Nearly 50% of the heavy minerals is classified in the 16–31 µm fraction, which determine the changes in the current research procedure traditionally used for Polish loess.