"Let me make one final plea, Mr. President," Budde said in her sermon, which lasted 15 minutes.
"Millions have put their trust in you. And as you told the nation yesterday, you have felt the providential hand of a loving God. In the name of our God, I ask you to have mercy upon the people in our country who are scared now," Budde said, turning her gaze towards the president.
Trump and his allies quickly criticized the bishop's remarks, with one Republican congressman saying that the American-born Budde should be "added to the deportation list."
Despite the backlash, Budde told NPR that her remarks were sincere, and she did not have any regrets in bringing them to the president's attention.
"I don't hate the president, and I pray for him," Budde said. "I don't feel there's a need to apologize for a request for mercy."
"I regret that it was something that has caused the kind of response that it has, in the sense that it actually confirmed the very thing that I was speaking of earlier, which is our tendency to jump to outrage and not speak to one another with respect," she continued. "But no, I won't, I won't apologize for what I said."
Budde's entreaty came just a day after Trump rolled out a series of executive orders to make good on some of his most controversial campaign promises, including one that amounts to the rejection of transgender identity, calling it a "false claim," and another that would seek to do away with birthright citizenship, which has already met legal challenges.
Budde said these orders and Trump's rhetoric have stoked fear among society's most vulnerable.
"There are gay, lesbian and transgender children in Democratic, Republican, and independent families, some who fear for their lives," Budde said.
"The people who pick our crops and clean our office buildings; who labor in poultry farms and meat packing plants; who wash the dishes after we eat in restaurants and work the night shifts in hospitals, they — they may not be citizens or have the proper documentation. But the vast majority of immigrants are not criminals. They pay taxes and are good neighbors."