A new generation of clay-based nano pigments has been introduced, providing the advantage of both inorganic pigments and organic dyes. These nano pigments have been synthesized through a stepwise procedure where, initially, an organic dye is adsorbed onto the surface of the adsorbent, and then dye adsorbed adsorbent is used as pigment for further applications. The objective of the current paper was to examine the interaction of non-biodegradable toxic dyes, Crystal Violet (CV) and Indigo Carmine (IC), with clay minerals (montmorillonite (Mt), vermiculite (Vt), and clay bentonite (Bent)) and their organically modified forms (OMt, OBent, and OVt) and to develop a novel methodology for the synthesis of the value-added products and clay-based nano pigments without creating second generation waste materials. In our observation, the uptake of CV was more intense onto pristine Mt, Bent, and Vt, and the uptake of IC was more onto OMt, OBent, and OVt. CV was found to be in the interlayer region of Mt and Bent, as supported by XRD data. Zeta potential values confirmed the presence of CV on their surface. In contrast, in the case of Vt and organically modified forms, the dye was found on the surface, confirmed by XRD and zeta potential values. In the case of indigo carmine, the dye was found only on the surface of pristine Mt, Bent, Vt, and organo Mt, Bent, Vt. During the interaction of CV and IC with clay and organoclays, intense violet and blue-colored solid residues were obtained (also known as clay-based nano pigments). The nano pigments were used as colorants in a poly (methyl-methacrylate) (PMMA) polymer matrix to form transparent polymer films.