The chemical modification of proteins has provided a toolbox enabling many experiments in chemical biology. However, new strategies are required to be able to specifically target (hetero)aromatic residues. Fluorine atoms installed in proteins can serve as useful tags, but methods for efficient and selective chemical fluorination are limited. This thesis has explored the modification of native residues in proteins with fluoroalkyl radicals to address the shortage in current methodologies. The study began with the investigation of trifluoromethylation, using biocompatible oxidative generation of CF3 radicals from a sulfinate precursor, and resulted in a robust protocol for selective modification of tryptophan residues. Proteins modified with this minimally perturbing tag could be readily studied by protein observed 19F NMR. To evaluate possibility of 18F-trifluoromethylation, the automated radiosynthesis of the radical precursor was achieved, but unfortunately, the protein radiolabelling proceeded with a limited efficiency. On the other hand, the study of protein difluoroethylation, using the same radical generation system, revealed an unexpected N-modification of proteins, for which the mechanism was proposed (oxidative hydrolysis of fluoroalkyl sulfinates). To reduce this side reactivity, an improved fluoroalkylation protocol was developed, based on the photoredox activation of heteroaryl sulfones as radical precursors. The platform was used to study reactivity and selectivity trends of various fluoroalkyl radicals, which resulted in the detailed investigation of difluoromethylation. The preference for the formation of unstable difluoromethyl tryptophan products was used for the development of selective C-formylation of proteins, relying on a key step of the denaturative hydrolysis of the CF2H group. As such, a new method was established for the installation of a masked aldehyde, also serving as a minimal size fluorescent probe. Overall, the studies of radical fluoroalkylation of proteins yielded useful methods for modification of typically solvent inaccessible residues (specifically tryptophan), under-targeted in protein chemistry, with applications in protein observed NMR and bioconjugation.