Most of Baltard's career was devoted to serving the City of Paris. His initial career undoubtedly benefited from the support of his father and his brothers in law, the architects Jaÿ and Lequeux, who had significant responsibilities in the Paris administration. But it was upon the recommendation of Ingres and his friend, the sculptor Gatteaux, a municipal councillor close to the prefect Rambuteau, that he obtained his first important position on his return from Rome in 1839: that of Inspector of Fine Arts, in charge of the decor in Parisian churches.
Appointed architect of the central covered markets in 1845, he then became the architect for the Hôtel de Ville and Churches of Paris (1848), then the architect for municipal festivals (1853). With the arrival of Haussmann, who he knew since childhood and who shared his Protestant faith, his career found a new and important support: in 1860, he was appointed to the head of the completely new architecture department of the City.
In the autumn of 1870, considering that his functions were too closely related to the regime which had just collapsed, Baltard left the services of the City.
On his return from Rome, the young Baltard sought to make his talents known. The competition for the tomb of Napoleon, launched in April 1841, was an exceptional occasion for this. His project, for which the drawings were recently found and which was based on the original idea of putting the tomb in an underground crypt under the Invalides church, came joint first, equal with that of Louis Visconti. Although the government finally preferred Visconti, who was more experienced, Baltard came out of this competition with his prestige enhanced.;
Napoleon's tomb would not be his only contribution in the field of commemorative architecture. Other than numerous tombs in Paris cemeteries, Baltard completed a project for the tomb of Monseigneur Affre, the Archbishop of Paris who died a heroic death in June 1848, and the moving commemorative monument dedicated to his friend Hippolyte Flandrin in the Saint-Germain-des-Prés church.