On his return to France, after several years working as an engineer building bridges, his first major commission, however, was to complete the Parisian Church of the Oratorians, (1616), which had been begun by Clément Métezeau; its success made his reputation.

In 1625 Richelieu put him in charge of the main royal project, the galleries being added to the Louvre, where Lemercier was working to the design established by Pierre Lescot a generation before; for the sake of regularity, Lescot's ranges in the Cour Carré were multiplied round further courtyards, quadrupling the building area, each of the four sides having a pavilion at its center.

Two superposed orders of columns and rich sculptural decor in pediments and niches, on piers and panels are kept under control by strong horizontal cornice lines.

During 1638 and 1639, Lemercier was appointed premier architecte charged with supervision of all the royal building enterprises, in which capacity he fell into a disagreeable dispute with the cultivated Nicolas Poussin about the decorations in the Louvre.

Only one remnant survives: a wall fragment with a relief of ship anchors and prows, signs of the Cardinal's role as Superintendent of the Navy, which appeared throughout the palace.

The hemispherical dome on a tall octagonal drum, first of its type in France, has four small cupolas in the angles of the Greek cross above the two Corinthian orders on the façade, of full columns below, flat pilasters above.

At the royal abbey church of Val-de-Grâce Lemercier succeeded the elder Mansart who completed the structure to the cornice line, and refused to agree to a change in the building's design.

the deep choir emphasizes the extent of the interior, scarcely interrupted by the discreet low dome over the crossing, which is hidden on the exterior beneath the transept roof.