One of the churches, St. David's Episcopal, in Beanblossom, Ind., was targeted sometime Saturday, a Facebook post from the church says.
"Three tags were painted on the outside of the church," the post says, including "Heil Trump" and a swastika.
"We are disappointed that our safe haven has been vandalized but will not let the actions of a few damper our love of Christ and the world," the statement says. "We will continue to live out our beliefs and acceptance of all people and respecting the dignity of every human being. We pray for the perpetrators as well as those who the derogatory marks were directed at."
Rev. Kelsey Hutto said "we must be doing something right," according to the Indianapolis Star. "We stated one time that doing the right thing was not always the popular thing. We were targeted for a reason, and in our mind it was for a good reason."
And in a statement, Indianapolis Bishop Cate Waynick said the tone of the election has "emboldened" some.
Separately, in an Episcopal church in Silver Spring, Md., a sign advertising the Spanish-language mass was vandalized with "Trump Nation, Whites Only," according to the Episcopal Diocese of Washington, DC.
"I am heartsick, and can only imagine how the people of Our Saviour, one of the most culturally diverse parishes in the diocese, feel," Bishop Marian Budde said in the Facebook post.
Earlier this month, a black church in Mississippi was vandalized with "Vote Trump" and burned.
Trump, for his part, has said he is the "least racist" person and, when questioned about the heated rhetoric that has flared up around the campaign, he told CBS News that he would tell perpetrators to "stop it."