AbstractCysteine‐based perfluoroaromatic (hexafluorobenzene (HFB) and decafluorobiphenyl (DFBP)) were synthesized and established as a chemoselective and available core to construct molecular systems ranging from small molecules to biomolecules with interesting properties. The DFBP was found more effective than HFB for the monoalkylation of decorated thiol molecules. As proof of concept of the potential application of perfluorinated derivatives as non‐cleavable linkers, some antibody‐perfluorinated conjugates were prepared via thiol through two different strategies, i) using thiol from reduced cystamine coupling to carboxylic acids from mAb by amide bond, and ii) using thiols from reduction of mAb disulfide bond. Conjugates cell binding analysis demonstrated that the bioconjugation does not affect the macromolecular entity. Besides, some molecular properties of synthesized compounds are evaluated through spectroscopic characterization (FTIR and ¹⁹F NMR chemical shifts) and theoretical calculations. The comparison of calculated and experimental ¹⁹F NMR shifts and IR wavenumbers give excellent correlations, asserting as powerful tools in structurally identifying HFB and DFBP derivatives. Moreover, molecular docking was also developed to predict cysteine‐based perfluorated derivatives’ affinity against topoisomerase Il and cyclooxygenase 2 (COX‐2). The results suggested that mainly cysteine‐based DFBP derivatives could be potential topoisomerase II α and COX‐2 binders, becoming potential anticancer agents and candidates for anti‐inflammatory treatment.