Carbon-fiber microelectrodes are proven and powerful sensors for electroanalytical measurements in a variety of environments, including complex systems such as the brain. They are used to detect and quantify a range of biological molecules, including neuropeptides, which are of broad interest for understanding physiological function. The enkephalins (met- and leu-) are endogenous opioid peptides that are involved in both pain and motivated behavior. Each is comprised of only five amino acids including tyrosine, an electroactive species. Electroanalytical measurements targeting tyrosine can reveal the dynamics of endogenous enkephalin transients in live tissue. However, when using electrochemistry in a biological system, selectivity is always a concern. Many larger neuropeptides also contain tyrosine. As such, they could generate a redox signature similar to that of the enkephalins, potentially confounding the measurement. In this work, three distinctly sized dioxythiophene monomers were mixed with Nafion and electrodeposited onto cylindrical carbon-fiber microelectrodes to form composite polymer films that allow for the tunable, size-based exclusion of larger molecules. The dioxythiophene monomers 3,4-ethylenedioxythiophene (EDOT), 3,4-propylenedioxythiophene (ProDOT), and 3,4-(2',2'-diethylpropylene) dioxythiophene (ProDOT-Et2) were used to create nanostructured pores of increasing size. The dioxythiophene/Nafion modified electrodes were characterized in the voltammetric detection of dopamine, a classic small molecule neurotransmitter, and a series of tyrosine containing neuropeptides of increasing size: met-enkephalin (M-ENK; 5 residues), oxytocin (OXY; 9 residues), neurotensin (NT; 13 residues), and neuropeptide Y (NPY; 36 residues). The modified electrodes exhibited enhanced selectivity for smaller peptide species over larger peptides in a manner consistent with the size of the dioxythiophene monomer incorporated into the polymeric film, allowing for tunability in terms of size-based selective detection.