Chaptal, the son of an apothecary from Nogaret, France, studied medicine at Montpellier, graduating in 1777. He later switched to chemistry, becoming professor at Montpellier in 1781. During the French Revolution he was arrested but then released to manage the saltpeter works at Grenelle. He also helped to organize the introduction of the metric system and published a textbook, Elémens de chimie (1790–1803).

Chaptal is mainly remembered as an industrial chemist; he was the first to produce sulfuric acid commercially in France at his factory at Montpellier. His early paper on bleaching (1787) was translated and published in England in 1790 by Robert Kerr. In 1800 he proposed a new method of bleaching using vapor from a boiling alkaline liquor, which was soon introduced into England. Chaptal also wrote one of the first books on industrial chemistry, Chimie appliquée aux arts (1807; Chemistry Applied to the Arts).