The company's previously donated millions to charities such as the Salvation Army and the Fellowship of Christian Athletes (FCA).
But the chain has been criticised for its perceived anti-LGBT stance along with accusations that those charities oppose same-sex marriage.
Last month, the first UK branch in Reading was told it wouldn't have its lease renewed after a backlash while a second store in Scotland has also faced opposition.
Owners now say they will now focus on three initiatives with one charity for each: education, homelessness and hunger.
Speaking to Bisnow, Chick-fil-A President and Chief Operating Officer Tim Tassopoulos said: "There's no question we know that, as we go into new markets, we need to be clear about who we are.
"There are lots of articles and newscasts about Chick-fil-A, and we thought we needed to be clear about our message."
The Chick-fil-A Foundation is reported to have donated $115K to the Salvation Army and $1.65M to the FCA in 2018.
The restaurant says it wants to ensure all customers feel welcome.
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