Hope Presbyterian Church hosts two congregations, one mostly white and one mostly Black.
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ABC 7 Chicago's news partner the Daily Herald reported that vandals wrecked a display of signs outside the church.
Those signs included messages of solidarity, including "Black Lives Matter."
"It's a painful lesson," church leaders said. "This action reminded us of where we are, but we also know that we need to be more cautious."
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Leaders of both churches hope to come together in the coming days to organize a vigil in support of the Black community.
Wheaton police said the damaged was reported Monday morning at about 6 a.m., when a dog walker saw the damaged signs. One of the signs was burned and was still smoldering.
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The church had previously experienced the theft of a "Black Lives Matter" sign, which was reported on Aug. 26, police said.
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The Wheaton Police Department is investigating both incidents.
"Damage to the property of a religious institution is a serious felony crime and will not be tolerated. Anyone participating in these crimes will be prosecuted to the fullest extent of the law," Deputy Police Chief P.J. Youker said.
Anyone with information about these incidents is encouraged to contact Wheaton police Lt. Bill Cooley at 630-260-2077.