Water-soluble functionalized carbon nanotubes (CNTs) have been prepared and further conjugated through a stable covalent bond with two peptidomimetics. The structural design of the covalently grafted peptidomimetics to the CNTs is based on their structural similarity with the metabolites of antagonist G of substance P. A variety of analytical spectroscopic methods, in combination with electron microscopy and thermal analysis, aided the structural and morphological characterization of the four newly synthesized peptidomimetic-CNT conjugates. It is demonstrated that the trypsin inhibitory effect of the peptidomimetic-CNT is enhanced as a result of the high-loading of peptidomimetics onto the skeleton of the modified water-soluble CNTs. Additionally, the peptidomimetic-functionalized CNT conjugates can be recovered and re-employed up to six biological evaluation cycles showing the same trypsin inhibitory activity. Such a nanosized system is extremely advantageous for the inhibition of inflammation or malignancy and could find potential future biological applications in the area of drug delivery systems.