Shikonin, a naphthoquinone dye, is a molecule of colour of natural origin, whose peculiar properties have not yet been fully rationalized. Its core structure consists of a di-hydroxy-naphthoquinone with an additional non-aromatic hydroxy group. From a comprehensive study involving fast spectroscopic techniques (fs-TA and fs-UC) and TDDFT electronic structure calculations on shikonin (Shk) and its derivatives 5-hydroxy-1,4-naphthoquinone (5HNQ), 5,8-diacetoxy-1,4-naphthoquinone (DiAc), 5,8-dihidroxy-1,4-naphthoquinone (DHNQ) and acetylshikonin, AcShk, it is shown that intramolecular excited state proton transfer (ESIPT) is present and is determinant in the deactivation of the hydroxy containing molecules. This is mirrored by the dominance of the internal conversion deactivation channel. In Shk, the non-aromatic hydroxy group determines the preferred conformer in both the ground- and excited-state, as reflected in the doubling of the fluorescence quantum yield value of this molecule relative to DHNQ. From fs-UC, a kinetic isotopic effect of 1.7 was obtained for DHNQ.