The synthesis, nanostructure self-assembly and electrochemical properties of a series of ferrocene conjugated peptides derived from the dipeptide Phe–Phe, a nucleoside and a peptide nucleic acid unit, which are covalently attached through a triazole linker, are described. The semiconducting nature of the ferrocene conjugated peptides in modified carbon electrodes suggested their potential use in novel capacitors and as biomaterials. To understand the effect of ferrocene substituents on C-/N-termini, a series of Phe–Phe derivatives were prepared and their self-assembled morphology and electrochemical properties were evaluated. Attachment of alkynes (propyne) at C-termini resulted in nanorods for Fc–Phe–Phe–propyne and in spherical structures after conjugation with a nucleoside and PNA. The formation of spherical particles from nanorods occurred after click conjugation at C-termini which clearly shows the effect of chemical modification on their self-assembly. The potential supercapacitor device-material was obtained after adhering the self-assembled peptide on carbon electrodes. Here, we attempted to further examine the effect of structure and properties by modifying the functional N- and C-terminus conjugated substituents on Fc–Phe–Phe through its self-assembly process. The morphological characterization of these ferrocene peptides was done via FESEM, AFM and DLS experiments. We studied the effect of ferrocene with the conjugation of a nucleoside and PNA on self-assembly. Further, we studied the electrochemical properties including cyclic voltammetry to calculate the capacitance of all the ferrocene conjugated peptides. The results point to a new direction in the study of the Phe–Phe motif to rationally engineer new functional nanoarchitectures involving rational design of short metallocene peptide-based biomaterials and biosensors.