Indigoid dyes are well known as vat dyes. In their oxidized dichetonic form they are stable and insoluble in water, whereas in their reduced form, commonly known as leuco, they are soluble in water and able to be attached to fabric for dyeing purposes. These blue dyes are usually easily detectable in art objects by means of Raman spectroscopy by adopting for analyses a laser line at a high wavelength, such as a 785 nm diode laser. Unfortunately, in ancient artworks, that are often highly degraded, it is not always possible to collect high quality Raman spectra, which makes the analysis and identification of these compounds particularly challenging. In this work, we present a tailor-made methodology for the extraction and the recognition of indigoid dyes in works of art, which exploits the solubility of these compounds in their reduced form. Excellent Raman and surface enhanced Raman spectroscopy (SERS) spectra of indigo were acquired after micro-extraction on ancient and reference textiles, confirming the reliability of the presented procedure. Moreover, the methodology has been applied also for the extraction of the indigoid dye Tyrian purple on a reference textile, showing excellent results. This analytical method has been found to be extremely safe both for the reference textiles and the investigated ancient textiles, thus being a promising procedure for the selective analysis and detection of indigoid compounds in objects of artistic relevance.