In summary, we have successfully developed a novel late-stage strategy to label fluorogenic peptides and proteins for real-time imaging of cellular trafficking. We have optimized the Cys-selective, Pd-mediated arylation of unprotected biomolecules with small benzodiazole fluorogens and demonstrated its utility for the rapid synthesis of linear and cyclic peptides with high yields and purities. Importantly, the resulting labeled peptides are stable under physiological conditions and show strong fluorogenic behavior in both intensity-based and FLIM measurements. We demonstrated the application of this labeling strategy in multiple CPPs (TAT, penetratin, and sC18) and one protein (mCCL2). SNBD-labeled biomolecules retained their physicochemical and bioactivity properties and were used in wash-free imaging experiments in live cells for in situ visualization of their uptake mechanisms, namely direct translocation, micelle-mediated internalization, and endocytic uptake. Furthermore, the FLIM analysis of the labeled CPP sC18-SNBD clearly detected its subcellular localization in the cell membrane, cytosol and nucleus, and indicated that this peptide can undergo direct nuclear translocation in live cells. Finally, we showed successful labeling and live-cell imaging of the chemokine mCCL2 in mouse macrophages, underscoring the applicability of this approach to a wide range of peptide and protein-based structures. This work constitutes an efficient strategy for direct fluorogenic labeling of intact peptides and proteins and holds potential for future studies of intracellular trafficking, drug delivery, and biological therapeutics.