Lindley was born at Catton, near Norwich, where his father, George Lindley, author of A Guide to the Orchard and Kitchen Garden, owned a nursery garden. He was educated at what was then Norwich Grammar School. His first publication, in 1819, a translation of the Analyse du fruit of L. C. M. Richard, was followed in 1820 by an original Monographia Rosarum, with descriptions of new species, and drawings executed by himself, and in 1821 by Monographia Digitalium, and by "Observations on Pomaceae", contributed to the Linnean Society. Shortly afterwards he went to London, where he was engaged by J. C. Loudon to write the descriptive portion of the Encyclopaedia of Plants.
In his labours on this undertaking, which was completed in 1829, and by arduous studying the pattern of characters, he became convinced of the superiority of the "natural" system of Antoine Laurent de Jussieu, i.e. a system that reflected the great plan of nature. This had to be distinguished from the "artificial" system of Linnaeus followed in the Encyclopaedia; the conviction found expression in A Synopsis of British Flora, arranged according to the Natural Order (1829) and in An Introduction to the Natural System of Botany (1831).
In 1829 Lindley, who since 1822 had been assistant secretary to the Horticultural Society, was appointed to the chair of botany in University College, London, which he retained until 1860; he lectured also on botany from 1831 at the Royal Institution, and from 1836 at the Chelsea Physic Garden. He began the flower show of the Society in the later 1830s.
Lindley described the plants collected on Thomas Livingstone Mitchell's expeditions of 1838, and wrote an Appendix to the Botanical Register of 1839 describing plants collected by James Drummond and Georgiana Molloy of the Swan River Colony in Western Australia. He played a large part in having Charles Moore appointed as Director of the Sydney Botanical Gardens.
During his professoriate he wrote many scientific and popular works, besides contributing largely to the Botanical Register, of which he was editor for many years, and to The Gardeners' Chronicle, in which he had charge of the horticultural department from 1841. He was a fellow of the Royal, Linnean and Geological Societies. He died at his house in Bedford Park near Turnham Green.
His son Nathaniel Lindley became a judge and was elevated as Baron Lindley.
Besides those already mentioned, his works include:
He is one of the fathers of orchid classification.