The illegitimate son of a Spanish nobleman, Juan, and a young freed black slave, Anna Velasquez, Martin grew up in poverty. He spent part of his youth with a surgeon-barber from whom he learned some medicine and care of the sick.At age 11 he became a servant in the Holy Rosary Dominican priory in Lima, Peru. Promoted to almoner, he begged more than $2,000 a week from the rich to support the poor and sick of Lima.

Martin had a great desire to go off to some foreign mission and thus earn the palm of martyrdom. However, since this was not possible, he made a martyr out of his body, devoting himself to ceaseless and severe penances. In turn, God endowed him with many graces and wondrous gifts, such as, aerial flights and bilocation. Established an orphanage and children's hospital for the poor children of the slums. Set up a shelter for the stray cats and dogs and nursed them back to health. Lived in self-imposed austerity, never ate meat, fasted continuously, and spent much time in prayer and meditation with a great devotion to the Holy Eucharist. When Martin had come to realize that Christ Jesus "suffered for us and that he carried our sins on his body to the cross, he would meditate with remarkable ardor and affection about Christ on the cross. He had an exceptional love for the great sacrament of the Eucharist and often spent long hours in prayer before the Blessed Sacrament. His desire was to receive the sacrament in Communion as often as he could.

Placed in charge of the Dominican's infirmary; known for his tender care of the sick and for his spectacular cures. His superiors dropped the stipulation that "no black person may be received to the holy habit or profession of our order" and Martin took vows as a Dominican brother in 1603.