Ligand-directed Ru(bpy)3 photocatalysts induce chromophore-assisted light inactivation (CALI) of target proteins under visible light irradiation in vitro and within cells. Here, histidine, methionine, and tryptophan residues were oxidized by the singlet oxygen (1O2) generated by Ru(bpy)3 with light. The addition of a tyrosyl radical trapper (TRT), such as N'-acyl-N,N-dimethyl phenylenediamine, inhibited peptide/protein oxidation and induced labeling on the tyrosine residue. This mechanistic study suggests that TRT scavenges 1O2, concomitant with the coupling reaction to the tyrosyl radical generated by Ru(bpy)3. Both CALI and labeling can be regulated by the Ru(bpy)3 photocatalysts in the absence or presence of TRT. Ligand-conjugated Ru(bpy)3 photocatalysts (local environmental single-electron transfer catalysts: LSCs) were used not only for target-selective protein labeling, but also for protein knockdown by CALI.