In the early 1960s, the idea of rearranging the forecourt of Notre-Dame was settled upon. In 1962, the Paris City Council decided to set up an underground parking lot there. Two years later, preventive excavations under the authority of the archaeologist Michel Fleury were carried out to unearth potential relics. These lasted until 1975 and were fruitful: "there appeared the remains of Gallo-Roman public baths, a section of the 4th-century wall, foundations of medieval houses, 18th-century buildings up to the Haussmann sewers." Their significance led to the decision in 1967 to preserve these ruins in the form of a museum crypt. However, uncertainties about the future of the forecourt itself led to the site being left under construction for several years, much to the frustration of Parisian officials. The site for the parking entrance was decided in 1970, west of the forecourt, near the entrance to the future crypt, designed in a discreet contemporary style. In 1973, Michel Fleury advocated extending it even further west on the forecourt, where the remains of Saint-Étienne Cathedral are buried. The public opening of the crypt was delayed to such an extent that the magazine Sites & Monuments wondered: "Will it be classified among myths or sea serpents$1". It was finally inaugurated in 1980, but underground excavations continued until 1988, with the archaeologist Venceslas Kruta unearthing the remains of a dock from the port of Lutetia.
From 2014, the crypt displays 3D reproductions of Paris through the ages. In 2016, as the Paris City Hall launched a competition to rejuvenate the Île de la Cité, urban architect Dominique Perrault suggested replacing the Notre-Dame forecourt with a giant glass slab to reveal the presence of the crypt to all passersby. This idea was eventually rejected by Emmanuel Grégoire, deputy mayor to the Mayor of Paris, Anne Hidalgo. However, a comprehensive redevelopment of the cathedral's surroundings remained scheduled for the 2020s, with the issue of better integrating the crypt with the surrounding monuments still being relevant.
Following the fire at Notre-Dame de Paris, the crypt was closed and did not open for the museum night the following month. Its reopening, delayed by the Covid-19 pandemic, took place in July 2021. In June 2022, Bas Smets won the competition to redesign the surroundings of Notre-Dame Cathedral after the fire. The project includes plans for the old parking area with a new entrance to the archaeological crypt of the Île de la Cité; the work is scheduled for 2024-2027.
The crypt contains numerous remains located in the south of the Île de la Cité, the historical heart of Paris. One can observe several elements ranging from the Gallo-Roman era to the 19th century. From the Gallo-Roman period, preserved items include a section of the wall from the ancient port of Lutetia, a Gallo-Roman public bath establishment with its heating system by hypocaust, and a part of the city wall from the early 4th century. The Middle Ages left behind the basement of the old chapel of the Hôtel-Dieu and the foundations of the houses on Rue Neuve-Notre-Dame. From the 18th century, there are the foundations of the Hospice des Enfants-Trouvés (Hospice for Foundling Children). The 19th century contributed the layout of the Haussmannian sewers. From 2000 to the end of 2012, the crypt was managed by the Carnavalet Museum. Since January 1st, 2013, it's been one of the fourteen museums of the city of Paris managed by the public administrative institution Paris Musées.