The natural dyes, and dye sources, in two seventeenth century Arraiolos carpets from the National Museum of Machado de Castro were analysed by high-performance liquid chromatography with UV-vis diode array detection (HPLC-DAD) and HPLC-mass spectrometry (LC-MS). Weld (Reseda luteola L.), indigo and spurge flax (Daphne gnidium L.) were found to be the dye sources, in agreement with original dyeing recipes collected during the nineteenth century. In order to fully characterize the plant sources, LC-MS conditions were optimized with plant extracts and the chromatographic separation and mass detection were enhanced. Extraction of the dyes, in the Arraiolos carpet samples, was performed using mild conditions that avoid glycoside decomposition. For the blues a dimethylformamide solution proved to be efficient for indigotin recovery. For all the other colours, an improved mild extraction method (with oxalic acid, methanol, acetone and water) was used, enabling to obtain the full dye source fingerprint, namely the flavonoid glycosides in the yellow dyes.