Indigo blue is a natural organic color from the Indigofera tinctoria plant. It is insoluble in water and does not require mordant to fix the color; therefore, due to its nature it can be considered as a pigment or dye. The identification of indigo in cultural heritage is very difficult due to the complexity of its chemical formula and the changes that it can undergo in certain conservation and exposition conditions. For this reason, characterization of possible degradation, transformation, and reaction processes is essential for its identification. In this study, multispectral imaging has been used for the first time as noninvasive technique to characterize the aging state of indigo blue using samples aged in a controlled climate chamber under extreme conditions of humidity, temperature, and light. The technique has proven to be very promising for this application, together with classification techniques based on machine learning approaches.