Among the bookshops of Tartu two nationwide chain stores Apollo and Rahva Raamat are represented. Since 2011, the Bookshop of the University of Tartu has been incorporated into the Internet bookshop Krisostomus trading in literature in foreign languages, which holds exhibition sales of the most recent scholarly literature in English and has also organised auctions of old and rare publications for bibliophiles and libraries. 

Although big chain stores have for a while been at the forefront of the book trade in several places all over the world, a movement in the opposite direction – the rebirth of small independent bookshops – has been noted and this is also the case in Tartu: in the Tartu Literature House a bookshop called Utoopia was opened in 2015, selling fiction as well as scholarly books. The popularity of the bookshop has grown rapidly and in addition to a choice of books, the shop also provides a pleasant environment for perusing books and organises a variety of events, including literary salons, discussions with writers etc. Trading in second-hand books also forms a notable part of book circulation. Second-hand bookshops are more numerous in Tartu than in any other Estonian town – there are several shops in the city centre and elsewhere. Among these, the Fahrenheit 451 Bookroom in the cultural factory Aparaaditehas at the Print and Paper Museum also organises literary events and is dedicated to collecting used books not needed any more and saving them from destruction.