Oligo(3-hexylthiophene-co-1,4-phenylene) and poly(3-hexylthiophene) were solubilized in sodium deoxycholate self-assemblies in water solutions and hydrogels, with the goal of solubilizing sufficient material in a hydrogel for fluorescence applications. The neutral conjugated oligomer and polymer were incorporated as monomers into the self-assemblies with sodium deoxycholate aggregates, leading to the photoprotection of these neutral conjugated and water-insoluble molecules. Dynamic light scattering, rheology, and fluorescence experiments established that the deoxycholate aggregation and gel formation properties were not altered with the incorporation of the oligomer or polymer into the deoxycholate self-assemblies, showing that this adaptable host system with some molecular recognition elements is a viable strategy to incorporate into hydrogels neutral conjugated molecules as isolated monomers. This strategy has the potential to be used when conjugated molecules are used for fluorescence applications in hydrogels.