Quarter then served as a curate at St. Peter's Church in Manhattan, and ministered to the sick and dying during the cholera epidemic of 1832. He placed the children who had been orphaned by the epidemic under the care of the Sisters of Charity. In 1833 he was named pastor of St. Mary's Church on Grand Street on the Lower East Side, where he founded a parochial school. He also received Maximilian Oertel, a Lutheran minister, into the Catholic Church in 1840.