Nine groups gave up grants totaling nearly $300,000.
The marriage bill stalled in the Illinois House after the Senate approved the measure on Valentine's Day. Debate on the issue is expected to return to Springfield on Tuesday as lawmakers reconvene for the fall session.
Jenny Arwade, executive director of the Albany Park Neighborhood Council, told the paper that it does not "have a formal stance on marriage equality."
"Our organizational values are that we believe in equal rights for all people," she said. "We were disappointed in the decision. We also believe it's the church's decision to do what they want to do."
Cardinal Francis George, Chicago's archbishop and a staunch opponent of marriage equality, defended the decision.
"Donors to the [Catholic Campaign] give to this anti-poverty organization with the understanding that their money will be passed on to organizations that respect the teachings of the Catholic faith," George said in an open letter in July. "Organizations that apply for funds do so agreeing to this condition."
An emergency fund set up to help the struggling groups has raised $91,000 toward closing the nearly $300,000 gap. Gill Foundation and Crossroads Fund are among the groups who have contributed to the Solidarity Fund.