In this paper we present a new theory to re-examine the immobilization technique of dye doped sol–gel films, define the strength and types of possible bonds between the immobilized molecule and sol–gel glass, and show that the immobilized molecule is not free inside the pores as was previously thought. Immobilizing three different pH sensitive dyes with different size and functional groups inside the same sol–gel films revealed important information about the nature of the interaction between the doped molecule and the sol–gel matrix. The samples were characterized by means of ultraviolet-visible spectrophotometer (UV-VIS), thermal gravimetric analysis (TGA), mercury porosimetry (MP), nuclear magnetic resonance spectroscopy (²⁹Si NMR) and field-emission environmental scanning electron microscopy (ESEM-FEG). It was found that the doped molecule itself has a great effect on the strength and types of the bonds. A number of factors were identified, such as number and types of the functional groups, overall charge, size, pK_a and number of the silanol groups which surround the immobilized molecule. These results were confirmed by the successful immobilization of bromocresol green (BCG) after a completely polymerized sol–gel was made. The sol–gel consisted of 50% tetraethoxysilane (TEOS) and 50% methyltriethoxysilane (MTEOS) (w/w). Moreover, the effect of the immobilized molecule on the structure of the sol–gel was studied by means of a leaky waveguide (LW) mode for doped films made before and after polymerization of the sol–gel.