Late-stage diversification of structurally complex amino acids and peptides provides tremendous potential for drug discovery and molecular imaging. Specifically, labeling peptides with fluorescent tags is one of the most important methods for visualizing their mode of operation. Despite major recent advances in the field, direct molecular peptide labeling by C–H activation is largely limited to dyes with relatively short emission wavelengths, leading to high background signals and poor signal-to-noise ratios. In sharp contrast, here we report on the fluorescent labeling of peptides catalyzed by non-toxic manganese(i)viaC(sp2)–H alkenylation in chemo- and site-selective manners, providing modular access to novel near-infrared (NIR) nitrobenzodiazole-based peptide fluorogenic probes.