Determination of composition and thickness is crucial for the preparation of thin layers. A separate measurement is possible, however, it could be time-consuming, and each technique requires a specifically prepared sample. Therefore, a combined, fast, and reliable technique would be advantageous. Calibration of energy dispersive X-ray spectroscopy (EDS) integrated with scanning electron microscope (SEM) by X-ray photoelectron spectroscopy (XPS), weighting balance and atomic force microscopy (AFM) were performed for simultaneous and non-destructive concentration, area density and thickness measurements of MnSi and MnGe thin layers prepared by a reactive pulsed laser deposition (PLD). The linearity of calibrations was supported by Monte Carlo calculations. The calibrations enabled the evaluation of Mn concentration with a deviation better than 2.7 at.%. The area density was determined with a deviation better than 6.8 µg/cm2, and the thickness was determined with a deviation better than 4.1 nm for samples measured with a standard substrate. The thickness measurement calibration omitting the standard substrate measurement resulted in the higher deviation of 7.6 nm, however, it enabled double sample throughput and spatial analyses.\n \n \n