In 2009, Whitney Houston revealed on The Oprah Winfrey Show (1986) that by the time The Preacher's Wife (1996) started shooting, her cocaine and marijuana habits had gotten so bad that there was never a day while filming the movie on which she had not done some drugs.
In a 2013 interview with the Archive of American Television, director Penny Marshall relayed a story where she had to ask one of the extras to leave during filming of one of the interior church scenes. She noticed that the person was wearing a yellow sweater, which was also the same color the church choir was wearing. Ironically enough, the sweater was provided by the production wardrobe assistants. Marshall found out, years later through a friend of hers, that the extra that she kicked out was future actress and comedian, Melissa McCarthy.
During filming at a church in Yonkers, New York, a building a block away caught on fire and two children were killed. A crew member was able to save one four year old child.
Most of the church scenes were filmed at Trinity United Methodist Church in Newark, New Jersey. The production renovated the church to look more like a Baptist church. After filming ended, more renovations were added to return the church to a Methodist style. In the film, the church needs a new boiler. In real life, the real church did need a new boiler. The money from the fees for renting the space helped the church buy a new boiler and ventilation system.