In 1541, Guy, Bishop of Megara, blessed the altars of the chapels of the apse. The same year, the parish awarded contracts for the windows and statues from Parisian artisans. The nave, from the Renaissance period, was not hunched before 1584. The first stone of the facade was laid in 1610 by Marguerite de Valois, who had agreed to do so in a personal donation of 3000 pounds.
The church was dedicated on February 25, 1626 by Jean-François de Gondi, first archbishop of Paris, Cardinal de Retz's uncle. Nevertheless, developments continued: in 1636, the organ was installed, the work of Pierre Pescheur.
In 1651, a new pulpit was installed. It was also adjusted for the local wardens and housing for the priests.
During the 17th and 18th century, the church of Saint-Etienne-du-Mont enjoyed great prestige. It was the scene of great processions where the shrine of Sainte-Genevieve went to Notre Dame and subsequently returned to his church. It also housed the remains of Pierre Perrault, the father of the author of Tales, the painter Eustache Le Sueur and Blaise Pascal. Those of Racine and Isaac de Sacy Lemaistre were also transferred in 1711 from Port-Royal in Saint-Etienne.