One of the best schools in pre-war Manila, the Jesuit-run Ateneo, established in 1859 and elevated to a secondary school in 1865, was located in Intramuros, a few minutes ride from home. But Leoni went to Saint Paul Institution at Calle Herran (now Pedro Gil Street) for the first two years of grade school. There he learned Basic English from French nuns. As to why his parents sent him to this school — something he himself wondered about all his life — it was because in 1921 Ateneo would only accept boys who had finished their first three primary grades. By 1923 due to requests from its alumni, the preparatory school offered grades from one to seven. In any case, Alfredo's decision for Leoni to study at the Ateneo followed family tradition. His father, brother, and he were Ateneans. His cousins graduated too from Ateneo.

By the time Leoni enrolled in June 1923, it had been three years since the American Jesuits of Maryland-New York Province took over the school from the Spanish Jesuits and introduced an English-based eight-year curriculum: a four-year high school and a four-year college leading to the Bachelor of Arts degree, with provision for drama and theatre as well as sports and athletics, and even military drill. English had become the lingua franca in business and government. Alfredo chose what he thought was best for Leoni. It was at the Ateneo that Leoni's budding Americanization was reinforced by his American teachers, the English-language curriculum, and his exposure to Catholic liturgy.

Almost everyone was a son of an Atenean in Leoni's third grade class where they were taught Christian doctrine in a half-hour class. Each month, he had to approach the sacraments of penance and the Eucharist so that by October 1923, he was admitted to the Sodality of the Virgin Mary. He learned to practise his First Friday devotions; undergo physical exercises every morning under the supervision of the physical director; and join in the games during recess or after class — a routine he would pursue in the coming years.