A native of Brescia, Italy, Aleni entered the Jesuit order in 1600 and studied astronomy under Christopher Clavius at the (Jesuit) Roman College. He reached Peking (Beijing) in 1613 and then accompanied Hsu Kuang-ch'i, the Christian convert who later became grand minister of the Ming dynasty, on his way to Shanghai. In 1619 Aleni was at Hangchow (Hangzhou) where he baptized 250 adults. At the invitation of Christians who had been baptized away from home but had returned to their native places, he opened new missions in Shansi (Shanxi) and Chekiang (Zhejiang) provinces.
He is best known for founding the Jesuit mission in Fukien (Fujian) Province in 1625. For four months he personally visited all the scholar officials of the capital city, Foochow (Fuzhou), and spent another eight months visiting all the other officials in the province. More than fifty scholars wrote testimonials praising Christianity. Forced to go to Macao because of persecution in 1638, he secretly returned to Fukien a year later. From 1641 to 1646 he was the Jesuit vice-provincial for southern China. He died at Yenping (Nanping) during the Manchu consolidation of Fukien province.