In 1819 Lindley arrived in London where, with the help of the botanist Sir William Jackson Hooker, he obtained a position as an assistant librarian. In 1822 he became garden assistant secretary at the Horticultural Society for which, in 1830, he organized the first flower shows to be held in England. He then served as the first professor of botany at the University of London (University College), where he remained until 1860.

Lindley's investigation in 1838 of the conditions at the Kew Gardens in London led him to recommend that the gardens be turned over to the nation and used as the botanical headquarters for the United Kingdom. His famous collection of orchids was eventually housed in the Kew herbarium. His Theory and Practice of Horticulture (1842) is considered to be one of the best books ever written on the physiological principles of horticulture. He developed his own natural system of plant classification for his best-known book, The Vegetable Kingdom (1846). Although his system was never adopted by other botanists, it did much to enhance the popularity of the natural system in England.