Gangsters raided and petrol-bombed Full Gospel Life Mission Church in Kirinyaga County on Saturday in an attack that has left residents baffled.
The motive for the attack on the church at Difathas village was not immediately established.
"We lost property worth more than Sh1 million. Nothing was salvaged," Reverend Isaack Kiringa said on Sunday, when about 200 worshippers attended a service outside.
"We never thought anyone could dare burn a church where people worship the living God. They did the unthinkable. They completely destroyed the church and left worshipers in the cold. They should repent.
Rev. Kiringa said they tried for hours to put out the fire but were unsuccessful as it spread fast.
"We were overwhelmed. It consumed everything including chairs and crosses. It was terrible," he said and appealed to police to bring the criminals to book.
Church treasurer Lydia Muthoni described the incident as an attack on God.
"They are fighting God but they will not succeed," she said. "This is the first such incidence since independence."
While noting that they had been peaceful, other worshipers said people against the spread of the Gospel may have been behind the fire.
"Outsiders plotted and executed their evil but the wrath of God will fall upon them," one said.
Kirinyaga East police boss Anthony Wanjuu asked residents to cooperate with them in the investigation.