During the early months of 1840, Adolphe Thiers' government formed a committee of twelve members (Commission des douze) to determine the location and design of a commemorative monument and choose an architect to execute the plan. The committee, which included notables such as Théophile Gautier, David d'Angers, and Jean-Auguste-Dominique Ingres, was chaired by politician Charles de Rémusat.
In April of that same year, the Commission des douze launched a competition for architects, which garnered 81 entries. These designs were showcased in the newly constructed Palais des Beaux-Arts. After a lengthy evaluation process, Louis Visconti was selected as the project's architect in 1842, and he finalized the monument's design by the middle of 1843.
Visconti designed an open crypt beneath the towering dome of the Invalides in a circular shape. The entrance to the crypt is flanked by two atlantes sculpted by Francisque Joseph Duret, and an inscription above the door recalls Napoleon's desire to be buried in Paris. A circular gallery surrounds the crypt, supported by twelve pillars decorated with victories sculpted by James Pradier until his death in 1852. Ten large relief panels on the gallery's wall celebrate Napoleon's achievements by Pierre-Charles Simart. Two additional panels by François Jouffroy commemorate the return of Napoleon's ashes. In the center of the crypt, a partly gilded statue of Napoleon in coronation attire by Simart stands in a cella.
The massive sarcophagus at the center of the crypt is often described as made of red porphyry, but it is actually made of purple quartzite from the Shoksha geological region near Lake Onega in Russian Karelia. The sarcophagus sits on a base of green granite from the Vosges, which, in turn, rests on a slab of black marble from Sainte-Luce. The project utilized stone from ten different quarries in and around France, as well as Carrara marble and the Russian quartzite.
The monument took years to complete due to the exceptional requirements for the stone used. The Russian quartzite was quarried in 1848 by Italian engineer Giovanni Bujatti with Tsar Nicholas I's special permission and shipped via Kronstadt and Le Havre to Paris. The sarcophagus was then sculpted by marbler A. Seguin using innovative steam-machinery techniques. The final stages of the project were delayed by the sudden death of Visconti in December 1853 and Napoleon III's alternative plan to move his uncle's resting place to the Basilica of Saint-Denis, which he eventually abandoned after commissioning plans from Eugène Viollet-le-Duc. Visconti was succeeded by Jules Frédéric Bouchet and, following the latter's death in 1860, by Alphonse-Nicolas Crépinet.
On 2 April 1861, Napoleon's remains were finally transferred into the sarcophagus from the nearby chapel of Saint-Jérôme, where they had rested since 1840. The ceremony was attended only by the Emperor Napoleon III, Empress Eugénie, the Prince Imperial Napoléon Eugène, other related princes, government ministers, and senior officials of the crown.
The Dome church completed the tombs of Napoleon's brothers shortly after. Jérôme Bonaparte's tomb was completed in 1862 and Joseph Bonaparte's tomb in 1864.
On December 15, 1940, the coffin of Napoleon II was moved from Vienna to be placed next to his father's tomb, following a decision made by Adolf Hitler and advice from his ambassador to France Otto Abetz. The initiative was intended to boost collaboration in the French public, but instead, it caused a political crisis in Vichy, leading to the abrupt dismissal of Pierre Laval by Philippe Pétain two days before the ceremony. On December 18, 1969, the coffin was transferred underground in the cella and covered by a marble slab.
In 2021, to commemorate the second centenary of Napoleon's death, French visual artist Pascal Convert created an installation called Memento Marengo. The installation features a synthetic copy of the skeleton of Napoleon's favorite horse, Marengo, which is preserved as a war trophy at the National Army Museum in London. The installation was placed above Napoleon's sarcophagus and has generated controversy despite being temporary in nature.