The synthesis of two chiral isomers of 3-substituted polythiophenes, with cationic side-chain functionalities, and their use as conformational sensitive optical probes for the recording of pH-induced conformational changes in a synthetic peptide are reported. The conformational changes of the synthetic peptide gives rise to geometrical changes of the conjugated polyelectrolytes, and these changes are shown as alterations of the absorption-, emission-, two-photon excitation emission and circular dichroism spectra of the conjugated polyelectrolytes. Interaction between a four-helix bundle conformation of the peptide and the conjugated polyelectrolytes will lead to a more planar conformation of the polyelectrolyte backbone and separation of polyelectrolyte chains, observed as a red shift and an increase of the emitted light from conjugated polyelectrolyte. As the peptide adopts a random-coil conformation, the intensity of the emitted light is further red shifted and the intensity is decreasing, associated with aggregation of the polyelectrolyte chains. Moreover, it is demonstrated how the specific chiral recognition can be quantified as differences in fluorescence emission based on both single- and two-photon excitation from the two enantiomeric isomers which interact differently with the peptide.