In 1829 Lindley was chosen the first professor of botany in the university of London (afterwards University College), an office which he held until 1860, when he was made emeritus professor. His lectures, delivered early in the morning, were clear, concise, and profusely illustrated, and attracted large classes. Among the more distinguished of his pupils were W. B. Carpenter, Edwin Lankester, and William Griffith. Lindley prepared diagrams and careful notes for his lectures, which were never formally read. In 1836 he succeeded Gilbert Burnett as lecturer on botany to the Apothecaries' Company at Chelsea, retaining the post until 1853.
It was on behalf of his pupils that many of his chief works were written. He was at all times a constant advocate of the natural as opposed to the Linnean system of classification, but, being engaged in original researches upon structure, he constantly changed his opinions upon questions of affinity, which perhaps lessened his immediate influence as a teacher.
Lindley was frequently consulted by government. Thus, in 1838, he reported on the condition of Kew Gardens, recommending that they should be made over to the nation, and should ultimately become the headquarters of botanical science for the empire. During the potato famine he was sent by Peel to Ireland, and he also advised as to the planting of the island of Ascension. He acted as juror in the exhibition of 1851 for food-products, and although he suffered then from the overwork entailed, he was persuaded in 1862 to take charge of the entire colonial department of the exhibition of that year. He found it necessary to resign his connection with the Horticultural Society, and a subscription was raised for a portrait of him, which was painted by Eddis, and hangs in the rooms of the society.
During the last few years of his life Lindley suffered from gradual softening of the brain, and on 1 Nov. 1865 apoplexy supervened, and he died in the house on Acton Green where he had lived for many years. He was buried in the Acton cemetery.
Lindley married in 1823 the daughter of Anthony Freestone of Southelmham, Suffolk, by whom he had three children. Two daughters assisted him in the illustration of some later works. His son, Sir Nathaniel, Lord Lindley, was a well-known judge. Lindley possessed most extraordinary energy and power of work. He was an enthusiastic member of the volunteer force, though he had lost the sight of one eye in infancy, and in spite of much sedentary work was remarkable for his erect bearing until the last. Hot-tempered and brusque in manner, he was very kind to young men, and incapable of a mean action.
Besides being a corresponding member of many foreign societies, Lindley was elected a fellow of the Royal Society in 1828, and received its royal medal in 1857, and in 1853 was chosen corresponding member of the French Institute. In addition to the oil portrait by Eddis already mentioned, there is a lithograph, taken in 1838, by J. Graf, in the ‘Naturalist,’ 1839 (iv. 434), and a later one in the series of honorary members of the Ipswich Museum, by Maguire. His name is commemorated in the genus Lindleya of the order Rosaceæ. His collection of orchids is preserved in the Kew herbarium, and the remainder of his herbarium at Cambridge.
Lindley planned a ‘Genera Plantarum,’ but abandoned the scheme on learning that the German botanist, Endlicher, was engaged upon a like work. Among his chief works were almost the whole of the descriptions in Loudon's ‘Encyclopædia of Plants,’ published between 1822 and 1829; all the botanical articles in the ‘Penny Cyclopædia’ as far as the letter R; ‘Synopsis of the British Flora,’ 1829, with editions in 1835 and 1859; ‘Introduction to the Natural System of Botany,’ 1830, of which the second edition appeared in 1836 as ‘A Natural System of Botany;’ ‘Outlines of Botany,’ 1830, and ‘Nixus Plantarum,’ 1833, revised and combined as ‘Key to Structural and Systematic Botany’ in 1835, this being again enlarged as ‘Elements of Botany’ in 1841; ‘Outlines of First Principles of Horticulture,’ 1832, enlarged into ‘The Theory of Horticulture,’ 1840, which, though translated into almost every European language, was not very successful in England until expanded in 1842 into ‘The Theory and Practice of Horticulture;’ ‘The Fossil Flora of Great Britain,’ in conjunction with William Hutton, 1831–7; most of vol. viii. and the whole of vol. ix. of Sibthorp's ‘Flora Græca,’ 1835–7; ‘Victoria Regia,’ 1837, a sumptuous volume, of which only twenty-five copies were printed; ‘Ladies' Botany,’ 1837–8, two volumes, written in the form of letters; ‘Flora Medica,’ 1838, followed in 1849 by ‘Medical and Œconomical Botany;’ the volume ‘Botany’ in the ‘Library of Useful Knowledge,’ issued by the Society for the Diffusion of Useful Knowledge, 1838; ‘School Botany,’ 1839; ‘Sertum Orchidaceum,’ a folio volume, with coloured plates by Miss Drake, completed in 1838; ‘The Genera and Species of Orchidaceous Plants,’ issued in parts, 1830–40, and partly reissued as ‘Folia Orchidacea’ between 1852 and 1859; ‘Orchidaceæ Lindenianæ,’
