Clinton was warmly received and drew her largest applause when pledged "to defend President Obama's legacy". That, she said, includes the Affordable Care Act, which has brought health insurance to 20 million additional people.
Clinton did not refer to Republican nominee Donald Trump by name, but she worked several jabs into her remarks delivered from the pulpit.
"We've got some serious issues to address, and the last thing we need is a loose cannon," she said, later adding: "The best way to repudiate a negative, hateful bigoted vision is by voting."
Clinton also suggested that she is the better prepared candidate.
"I know how hard it is to be president," the former Secretary of State and former first lady said. "I worked for one. I lived with another."
Citing scripture at several points in her remarks, Clinton urged the congregation to obey the commandment to "love our neighbours as ourselves".
"One thing we have to do in our country now is to make sure that everyone who is equal in God's eye is equal in our eye," she said.
The church visit was one of several planned several stops in the Miami area and in Broward County, including an afternoon "unity rally" in Wilton Manors.
Before heading to church., she dropped in on an early voting brunch sponsored by two Democratic groups in Miami at Fado's, an Irish pub.
"These last nine days we can really race to the finish line," Clinton told a crowd of about 40 people, who she urged to help elect Democrats up and down the ballot
"If any of you know anyone who is thinking about voting for Trump, I want you to stage an intervention," Clinton added. "Because friends don't let friends vote for Trump."