In 1749, the cathedral ended the tenure of its lackluster chapel master, Domingo Dutra, and announced it would seek a more able leader.
Jerusalem auditioned for the post.
The jury, steeped in traditional musical forms, resisted the modernity and eclecticism of his compositions but ultimately confirmed him as the new chapel master on November 3, 1750, a position Jerusalem held for the rest of his life.
The following decade proved tumultuous for Jerusalem: he became embroiled in a lawsuit with the tenant of the Coliseo, Joseph Calvo; his estranged wife, Doña Antonia de Estrada, petitioned the cathedral to garner his wages; he used his position to prevent musicians in other parishes from taking job opportunities from musicians in his parish; and he acquired a professional rival in Matheo Tollis della Rocca, who later succeeded Jerusalem as chapel master.
Yet Jerusalem counted a number of triumphs during this time: he modernized musical notation by cathedral copyists; he improved the quality of texts used in compositions of sacred music; he more than doubled the size of the cathedral orchestra; and he composed prolifically.
When he died on December 15, 1769, Jerusalem was highly esteemed by his colleagues and the musical community of Mexico City.
Along with other mid-century transplants from Spain, Jerusalem helped establish the Italianate galant style in Mexico, displacing older Spanish-style music; contrary to popular belief, he did not pay any attention to the native folk songs and instruments of Mexico.
His compositions circulated widely throughout New Spain (present-day Mexico) and Guatemala, reaching as far north as the California missions, where it found a place alongside the much simpler "California mission style" music.