The prior wooden church building, on East Government near the present-day Jefferson Street (five blocks to the southeast), had been destroyed by fire in September of 1882 during a raging yellow fever epidemic. Several months prior to that, however, Father John Baptist Baasen, pastor from 1882 to 1900, had purchased the property on Palafox Street for $3,000.

The new location was in an area where much building was being done, including a new courthouse on the opposite corner. The Methodist Church was at the other end of the block on the corner of Palafox and Garden, and the Lutheran Church was just another block away on the corner of Baylen and Garden Streets. Nonetheless, many members of the congregation objected to the new location being "so far from town"!

The church was constructed at a cost of $27,000. The exterior walls were of the very best red brick made in Kehoe's brickyard (but have since been covered with stucco). The interior woodwork was all Florida pine, stained and polished. Pews, with the date stamped on the bottom of each, were added in 1897.

During the early part of 1900, a number of improvements were made to the church, including a new organ. Large, life-like Stations of the Cross, all memorials bearing the names of pioneer Catholic families of Pensacola, were added. These were made of a type of papier-mâché and horsehair on a wire frame, and painted in full color. (Due to deterioration from a leaking roof, they were later stripped, sealed and covered with a marble-like coating.)

Art glass windows with ecclesiastical symbols were installed when the church was built and some of these were destroyed during the 1896 hurricane. Sometime after 1906, during the pastorate of Father Robert Fullerton, they were all replaced. These magnificent new stained glass windows collectively form one of the artistic treasures of Pensacola. They were designed and produced by Emil Frei, whose work is recognized as an unsurpassed example of the Munich Style of Pictorial Stained Glass. The Bavarian-born Frei studied at the Munich School of Fine Arts before immigrating to the United States in the 1890s. In 1898 he opened the Emil Frei Art Glass Company in St. Louis and was quickly recognized for his talent and skill. Frei created his masterpieces from lead crystal glass painted, detailed and fired to create strong, vibrant, high translucency colors with subtle gradations of hues and textures. The windows were severely damaged during the devastating hurricane of 1926, but were later fully restored by a team of master restorers in 1960. In 1954, the north tower entrance of the church was closed to construct a baptistery, and a new stained glass window with the text of the Apostles' Creed was placed there. In 1972, some of the windows were releaded, and all were covered on the outside with protective covers to stormproof and shatterproof them.

Many of the original furnishings from 1886 are still in use, including the beautiful carved wood altars, which were a gift from Mr. and Mrs. Francis Celestino Brent. Father John Baasen donated the church bell from funds inherited from his parents.

Prompted by changes in liturgical regulations of the Second Vatican Council, a major renovation of the church was begun in 1962. With the goal of saving the architectural beauty of the original sanctuary, the back wall was rebuilt in a straight line, removing the angles and increasing the size of the sanctuary. The tabernacle and table of the main altar were removed, and the vacant places were replaced by panels that were exact duplicates in style and carving of the balance of the altar. The back upper portion of the altar remained intact, forming a 'reredos' for the celebrant's chair while, at the same time, preventing any disproportion of height in the sanctuary. A new marble table of sacrifice was designed, which enabled the priest to celebrate Mass facing the people. The unique bowed altar rail was preserved, as Vatican Council II permitted "works of art" to remain.

As the 100th anniversary of the church building approached in 1986, plans began to restore the church to celebrate the centennial of the building. The ceiling was cleaned and revarnished; plaster was painted; red carpet was removed from the sanctuary area and replaced with white Alabama marble; new Spanish tile was installed in the aisles, and the pews and pine floors beneath them were refinished. The old organ was upgraded and the chest of pipes was placed on each side of the large stained-glass rose window of Saint Michael. The ranks of pipes were increased to 18, with a space for three additional ranks.

In June 1986, the restored church was rededicated at a Mass attended by an overflowing crowd. Archbishop Oscar H. Lipscomb, a well-known historian and the Archbishop of Mobile, delivered the homily.

The year 2004 brought two significant changes to St. Michael's. In July, we welcomed our new pastor, Father Peter A. McLaughlin. Almost before he could settle in, however, Hurricane Ivan devastated our community, nearly destroyed the rectory, and caused major damage to the church. Over the next year and a half, Father Pete tirelessly oversaw the reconstruction efforts, which included a new copper roof for both the church and the rectory. Finally, in April 2006, the last piece of scaffolding was removed just in time for the Easter celebration.