Spanish Missionary priests first introduced the Catholic Faith to native residents of Boerne, and over time, Catholic families of European decent, mostly from German lands, arrived in the frontier town of Boerne. These people were shepherded in faith by the priests who would travel from the San Fernando Cathedral to visit them in their homes, celebrating the Mass and sacraments with them. In the early 1860's, Bishop Claude Dubuis of the Galveston Archdiocese sent Emil Fleury, a new young deacon who wanted to become a priest, to build the first Catholic Church in Boerne.

Fleury found a spot high on a hill south of Cibolo Creek, and began to build the original St. Peter's Catholic Church. He poured all his time and strength into putting in those first church walls and was helped in his efforts by George Wilkens Kendall, the namesake of Kendall County and whose wife was Catholic. In 1866, Fleury presented the church to the Bishop of Galveston, complete and ready for use, and through some creative trading and backbreaking effort, debt-free. The Catholic families of Boerne worshipped in the first church for many years.

By 1920, approx. 50 families in the parish had outgrown that original church and construction began on a new, larger church. Built in the style of the Spanish Missions, this beautiful new church, modeled after San Antonio's Mission Conception, was completed in 1923. During construction, Emil Fleury, who was then a priest and a venerable man in his 70's, was on hand to lay the new cornerstone.

St. Peter's parish has continued to grow in exponential numbers. With great joy and after much hard work and dedication, St. Peter the Apostle celebrated the dedication of its third new worship space on October 17, 1999. The new space seats more than 800 people.