Trifluoroacetic acid is widely used as a reagent and solvent in organic synthesis. It is particularly effective in deprotection reactions, such as removing tert-butyloxycarbonyl (Boc) and tert-butyl ester protecting groups in peptide and nucleotide synthesis. Due to its strong acidity and volatility, it can be easily removed after reaction completion, making it ideal for purification processes.

It serves as a catalyst in esterifications, acylations, and polymerizations. In chromatography, especially HPLC, TFA is commonly used as an ion-pairing agent in mobile phases to improve the separation of polar and basic compounds.

TFA is also employed in the production of pharmaceuticals, agrochemicals, and liquid crystals, where it helps in the synthesis of fluorinated compounds that exhibit enhanced stability and bioavailability. Its ability to stabilize reactive intermediates makes it valuable in the preparation of specialty chemicals and fluorinated building blocks.