Synopsis Coloration is a complex phenotypic trait involving both physical and chemical processes at a multiscale level, from molecules to tissues. Pigments, whose main property is to absorb specific wavelengths of visible light, are usually deposited in specialized organelles or complex matrices comprising proteins, metals, ions, and redox compounds, among others. By modulating electronic properties and stability, interactions between pigments and these molecular actors can lead to color tuning. Furthermore, pigments are not only important for visual effects but also provide other critical functions, such as detoxification and antiradical activity. Hence, integrative studies of pigment organelles are required to understand how pigments interact with their cellular environment. In this review, we show how quantum chemistry, a computational method that models the molecular and optical properties of pigments, has provided key insights into the mechanisms by which pigment properties, from color to reactivity, are modulated by their organellar environment. These results allow us to rationalize and predict the way pigments behave in supramolecular complexes, up to the complete modeling of pigment organelles. We also discuss the main limitations of quantum chemistry, emphasizing the need for carrying experimental work with identical vigor. We finally suggest that taking into account the ecology of pigments (i.e., how they interact with these various other cellular components and at higher organizational levels) will lead to a greater understanding of how and why animals are vividly and variably colored, two fundamental questions in organismal biology.