Although de Candolle was descended from one of the ancient families of the Provence, he was born in Geneva as religious persecution had forced his ancestors to leave their native country in the middle of the 16th century. Despite being a sickly boy he showed great aptitude for study, and distinguished himself at school by his rapid attainments in classical and general literature, and specially by a faculty for writing elegant verse. He began his scientific studies at the college of Geneva, where the teaching of J.P.E. Vaucher first inspired him with the determination to make botanical science the chief pursuit of his life.

In 1796 he moved to Paris. His first productions, Plantarum historia succulentarum (4 vols., 1799) and Astragalogia (1802), brought him to the notice of Georges Cuvier, for whom he acted as deputy at the College de France in 1802, and of Jean - Baptiste Lamarck, who afterwards entrusted him with the publication of the third edition of the Flore française (1803 - 1815). The "Principes élémentaires de botanique", printed as the introduction to this work, contained the first exposition of his principles of classification, following a natural method as opposed to the artificial, Linnaean method.

In 1804 he was granted the degree of doctor of medicine by the medical faculty of Paris, and published his Essai sur les propriétés médicales des plantes, and soon after, in 1806, his Synopsis plantarum in flora Gallica descriptarum. At the request of the French government he spent the summers of the following six years in making a botanical and agricultural survey of the entire country, the results of which were published in 1813. In 1807 he was appointed professor of botany in the medical faculty of the university of Montpellier, to transfer in 1810 to the newly founded chair of botany in the faculty of sciences in the same university.

From Montpellier, where he published his Théorie élémentaire de la botanique (Elementary Theory of Botany, 1813), he moved back to Geneva in 1816 and in the following year was invited by the government of the Canton of Geneva to fill the newly created chair of natural history. The rest of his life was spent in an attempt to elaborate and complete his natural system of botanical classification. The results of his labours were initially published in his Regni vegetabilis systema naturale, but only two volumes were completed (1821) when he found that it would be impossible for him to complete this, at the chosen, extensive scale. Accordingly, in 1824 he began a less extensive work of the same kind, the Prodromus Systematis Naturalis Regni Vegetabilis, but even of this he was able to finish only seven volumes, or two thirds of the whole. He was elected a member of the Royal Swedish Academy of Sciences in 1826. He had been in delicate health for several years when he died at Geneva on 9 September 1841.

He is remembered in the genera Candollea and Candolleodendron. His son, Alphonse de Candolle, eventually succeeded to his father's chair and continued the Prodromus.

Augustin Pyramus de Candolle was the first to put forward the idea of "Nature's war", writing of plants being "at war one with another" with the meaning of different species fighting each other for space. Charles Darwin studied de Candolle's "natural system" of classification in 1826 when at the University of Edinburgh, and in the inception of Darwin's theory in 1838 he considered "the warring of the species", adding that it was even more strongly conveyed by Thomas Malthus, producing the pressures that Darwin later called natural selection. In 1839 de Candolle visited Britain and Darwin gave him dinner, getting the opportunity to discuss the idea.