With regard to the increasing number of tattooed people, legal regulations for tattoo inks were implemented across Europe-aiming for higher consumer safety. To control the laws' abidance, analytical methods are needed to identify banned ingredients from the given negative lists. Since specific organic pigments are often associated with tattoo side effects, their identification in tattoo inks as well as in biological samples is of great importance. Particularly, poorly soluble organic pigments are challenging to detect. In the past, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was reported as a promising tool for organic pigment identification. Here, we present a MALDI tandem mass spectrometry (MS/MS) approach to increase identification specificity and sensitivity in the process based on pigment fragment ions which is of special importance in tissue samples. For further verification of pigment identities, alkali metal cation attachment was used. Sample preparation was optimized and included mechanical disruption followed by the application as dried droplets with the matrices α-cyano-4-phenylcinnamic acid and sinapinic acid as well as ethanol. Pigments were identified by spectral comparison to reference libraries containing 40 pigments and following a decision tree. Additionally, successful pigment identification in biological samples was carried out. The implemented automated MALDI-MS and -MS/MS acquisitions make the hereby proposed pigment identification suitable for routine application.