X-ray fluorescence (XRF) analysis is a widely applied technique for the quantitative analysis of thin films up to the μm scale because of its non-destructive nature and because it is easily automated. When low uncertainties of the analytical results in the few percent range are required, the non-linear secondary fluorescence effect in multi-elemental samples may complicate an otherwise straightforward quantification, since it can easily exceed a relative contribution of 20%. The conventional solution, to rely on good performing reference samples, is hindered by their low availability, especially for thin film applications. To address this challenge, we demonstrate a flexible production method of multilayered, alloyed thin films with significant secondary fluorescence contributions. We use reference-free XRF analysis to validate the reliability of the physical model for secondary fluorescence, which includes a thorough uncertainty estimation. The investigated specimens are qualified as calibration samples for XRF or other quantitative analyses.