Selective removal of an organic compound in the coexistence of other constituents is a great challenge in separation and purification processes. In this work, bovine serum albumin (BSA)-stabilized iridium nanoparticles (IrNPs) were prepared via a facile one-step precipitation method. The resulting BSA–IrNPs were comprehensively characterized by TEM, XRD, XPS, UV–vis, FT-IR, and fluorescence spectroscopy as well as circular dichroism spectrometry. It was found that the nanoparticles with an average diameter of 3.6 nm were embedded in the aggregated protein matrix and the structure of the coating agent was maintained well on the surface of nanoparticles. The as-prepared nanozymes (BSA–IrNPs) exhibit strong peroxidase-like activity and can selectively catalyse the degradation of cationic compounds by H₂O₂ in the coexistence of other inorganic or organic substances at room temperature. Interestingly, the degradation of amino acids could be precisely controlled by adjusting the pH above or below their isoelectric points. The catalytic selectivity of BSA–IrNPs should be ascribed to the anchoring effect between the amidogen-containing molecules and BSA through electrostatic adsorption. The nanozyme also exhibits excellent reusability as it can be readily recycled from solution by static settlement or centrifugation. Therefore, BSA–IrNPs have great potential for the selective removal of cationic compounds and amino acids in a complex matrix.