One tornado touched down in Van Buren County, about 75 miles north of Little Rock, damaging at least 33 homes and injuring three people.
The twister demolished the sanctuary, a fellowship area, classrooms and a pavilion at Botkinburg Foursquare Church, its pastor said.
"If the tornado would have come an hour and a half later, we would have been caught in it," said Senior Pastor Ester Bass, referring to Wednesday night services.
No members of the church were injured.
But a passing motorist who parked his truck in the church's covered driveway to get out of the dangerous weather had a close call when the storm struck.
"It shook the truck and just lifted the roof right off the drive-through," said Bass. "He was all right."
Bass, 63, said his congregation of about 100 was left stunned.
"It is just devastating. My wife and I are just torn," he said. "We put a lot of sweat and hard work and it was paying off. The church was growing."
As church leaders prepared to meet with their insurance adjuster, the pastor was thankful for a loyal membership.
"They will be with me," he said. "They are ready to buckle down and do what we have to. With the Lord's help, we are going to rebuild."