Portable micro-X-ray fluorescence (micro-XRF) spectrometers mostly utilize a polycapillary X-ray lens along the excitation channel to collect, propagate and focus down to few tens of micrometers the X-ray tube radiation. However, the polycapillary X-ray lens increases the complexity of the quantification of micro-XRF data because its transmission efficiency is strongly dependent on the lens specifications and the propagated X-ray energy. This feature results to a significant and not easily predicted modification of the energy distribution of the primary X-ray tube spectrum. In the present work, we propose a simple calibration procedure of the X-ray lens transmission efficiency based on the fundamental parameters approach in XRF analysis. This analytical methodology is best suited for compact commercial and portable micro-XRF spectrometers. The developed calibration procedure is validated through the quantitative analysis of a broad range of samples with archeological relevance such as glasses, historical copper alloys, silver and gold alloys offering an overall accuracy of less than 10%-15%.