Linnaeus' botanical and zoological collections were purchased in 1783 by Sir James Edward Smith, the first President of the society, and are now held in London by the society. The collections include 14,000 plants, 158 fish, 1,564 shells, 3,198 insects, 1,600 books and 3,000 letters and documents. They may be viewed by appointment and there is a monthly tour of the collections.

Smith's own plant collection of 27,185 dried specimens, together with his correspondence and book collection, is also held by the Society.
Other notable holdings of the society include the notebooks and journals of Alfred Russel Wallace and the paintings of plants and animals made by Francis Buchanan-Hamilton (1762–1829) in Nepal.

In December 2014, the society's collection was added to the list of nationally significant collections in England by the Arts Council England.

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