He was martyred in Japan on February 5, 1597, alongside twenty-five companions, for preaching Christianity in defiance of the orders of Taiko Toyotomi Hideyoshi.

He initially served as a missionary in Mexico and later in the Philippines. In 1593, he was sent to Japan as a commissary for his order. There, he established churches and hospitals and converted many to Christianity.

However, due to growing religious unrest and political upheaval—exacerbated by the stranding of a Spanish vessel in Japan, which led to suspicions that missionaries were preparing for conquest—Hideyoshi ordered their arrest. Peter Baptist and his companions, including three Jesuits and fifteen members of the Third Order, were publicly paraded, had parts of their ears mutilated, and were taken to Nagasaki, where they were crucified.

They were canonized as saints in 1862 by Pope Pius IX and are collectively known as the Martyrs of Japan