An extremely stable hybrid composite, useable as a pigment in the Cultural Heritage and Materials Science fields, can be obtained by grinding and heating 2 wt% methyl red with palygorskite, a fibrous microporous clay mineral. Dye molecules are incorporated within the clay nanotunnels and/or superficial grooves, partly sheltered from the external environment and forming specific host–guest interactions that stabilize the composite. The molecular structure and surrounding interactions of the encapsulated methyl red molecules were studied by means of Fourier transform (FT) and surface‐enhanced Raman (SER) Spectroscopies – useful techniques to analyze adsorbates even at very low concentrations. Comparison between Fourier transform and SER spectra of the pristine dye and the hybrid composite shows that methyl red exists, after encapsulation in palygorskite, in its neutral (azo) and protonated (hydrazo) forms, both with planar morphology. Incorporation in the host framework favours significant transformation of the guest dye molecule from the azo to the hydrazo species, consistently with the composite synthesis being performed in acidic environment. The incidental addition of plasmonic substrates, used in SER spectra to enhance the Raman signal, further accentuates this conversion. Diffusion in the clay nanotunnels is expected to cause moderate ring deformations/distortions in the methyl red molecule, as reflected by the perturbation of selected Raman modes. The details about the specific orientations and interactions of the dye with the Ag colloid are discussed, as well as their effects on the Raman signal enhancement. Although a feasible quantification of their mutual amounts is impracticable, because of the too many variables involved, presence of several dye species in the host framework, each contributing to the nanocomposite colour, qualifies the studied complex as a polyfunctional organic/inorganic hybrid composite. Copyright © 2016 John Wiley & Sons, Ltd.