On August 5, 1913, Shigeo Iwanami, who was born in a farm family in Nakasu Village, Suwa County, Nagano Prefecture (now Nakasu, Suwa City, Nagano Prefecture), was born in 16 Minami Jimbocho, Kanda Ward, Tokyo (now Chiyoda Ward, Tokyo). Kanda Jimbocho) opened a second-hand bookstore, named "Iwanami Shoten", with the "urn" (かめ) drawn by Hashiguchi Goha as the first generation trademark. It attracted much attention at the time because of its "open price selling" method. In September 1914, Iwanami Shoten published Natsume Soseki's novel "Heart", officially entering the publishing industry. On January 1, 1916, the first commemorative photo was taken at Iwanami Shoten. After Soseki's death, they published "The Complete Works of Natsume Soseki" and achieved rapid development. Their signboard was also inscribed by Soseki himself.

On February 5, 1920, Iwanami Shoten purchased a three-story building on Imagawakoji, Kanda-ku, Tokyo, and moved the publishing department of Iwanami Shoten there to serve as a warehouse. On September 1, 1923, the Great Kanto Earthquake occurred in Japan. Iwanami Shoten's headquarters (and main store) in Minamijimbocho, its sales department (and warehouse) in Imagawakoji, and the printing factory in Yurakucho were destroyed by fire, with losses of approximately 800,000 yen, all 22 Iwanami Bookstore clerks and 8 members of the Iwanami family are safe. After the fire, the Iwanami Bookstore headquarters was rebuilt on the same site, and the sales department sold both used and new books.

On October 9, 1929, the editorial office of Iwanami Shoten moved to the former Tokyo University of Commerce (restructured into Hitotsubashi University in 1949) building in Hitotsubashi. It was a reinforced concrete structure with two floors above ground. The total area is 249.4 square meters; later, a third floor was added to the top floor, and the dictionary and correction departments moved to the third floor. On December 10, 1933, Iwanami Shoten took the manuscript from the painting "The Sower" by French painter Jean-Fran?ois Millet. Kojima Kikuo's second-generation trademark was processed by the poet and sculptor Kotaro Takamura as the store's seal. Iwanami Shoten was the first to use the second-generation trademark in the "Iwanami Complete Book" series launched on the same day. On February 5, 1934, Iwanami Shoten published Hashida Kunihiko's "Bitan Shu", using the second-generation trademark for the first time in a single volume.

On January 13, 1940, the Ministry of Internal Affairs ordered Iwanami Shoten to report on the printing and binding status of Tsuda Sōyoshi's works. On January 21, 1940, Iwanami Shigeo was summoned by the Tokyo District Prosecutor's Office (today's Tokyo District Prosecutor's Office) to question Tsuda Sōyoshi's works from the morning to 17:30 in the afternoon. On January 24, 1940, the Metropolitan Police ordered Iwanami Bookstore to report the inventory of Tsuda Sōyoshi's works. On January 31, 1940, Iwanami Shoten reported the inventory of Tsuda Sōyoshi’s works to the Tokyo District Public Prosecutor’s Bureau. On February 3, 1940, the Tokyo District Prosecutors' Bureau ordered Iwanami Shoten to submit a report on the issues related to Tsuda Sōyoshi's works. On February 10, 1940, Tsuda Sōyoshi's "Research on Kojiki and Nihon Shoki" (Research on Kojiki and Nihon Shoki) published by Iwanami Shoten was banned and impounded. On February 12, 1940, two books by Tsuda Sōyoshi, "Research on the History of the Gods" (Research on the History of the Gods) and "Society and Thought of Predecessor Japan" (Society and Thought of Predecessor Japan) published by Iwanami Shoten were banned. On March 8, 1940, Tsuda Sōyoshi and Iwanami Shigeo were prosecuted by prosecutors in accordance with Article 26 of the Publication Act (Law No. 15 of April 14, 1940) for the "Tsuda Incident." In May 1942, Tsuda Sōyoshi was sentenced to 3 months' imprisonment, and Iwanami Shigeo was sentenced to 3 months' imprisonment, both of which were suspended for 2 years; Tsuda Sōyoshi appealed. In 1944, the case, which was under appeal, was ruled not to be prosecuted because the statute of limitations had expired.

In September 1945, Iwanami Shigeo fell ill due to cerebral hemorrhage and stayed at the Iwanami family's villa "Sukikiso" in Izuyama, Atami City. On April 25, 1946, Iwanami Shigeo passed away at the age of 64. His religious title was "Bunyouin Godo Munege Lay Buddhist". On April 25, 1949, Iwanami Shoten was reorganized into a limited company, and its president was no longer hereditary from the Iwanami family.

In August 1990, Iwanami Bookstore demolished its old headquarters and rebuilt the original site into the Iwanami Bookstore headquarters building.