Keramlis, a town on the Nineveh plains, was captured by ISIS in August 2014.
The town was retaken by Iraqi forces three weeks ago as part of the Mosul offense.
Many of Keramlis' residents have been living in camps in Iraq's Kurdish region.
Some returned on Sunday to attend a prayer service at the St Addai church.
ISIS militants had decapitated a statue of the Virgin Mary before they left the town.
Tombs outside the church had been vandalised, windows smashed and pews burned.
Before the start of the service, led by Rev Thabet Habib, the church bell was tolled for the first time in more than two years.
"It was amazing, I got goose bumps. The bell for us means a great deal," Sahir Shamoun said.
Mr Shamoun and his wife visited their former home in the city. They found the place ransacked and their electronics and furniture stolen.
"I feel great sadness," he said. "I'm not sure when or if I'll be back. I think of my children, will they have a future here?"
Mr Shamoun also said he believes there is no future for Christians or minorities in the Middle East.
"You put the cornerstone for your home, but still you know it's not yours," he said. "But we are stubborn people, we will keep building."
Christians once made up a sizable minority in Iraq. ISIS is believed to have killed over a thousand Christians in the last two years, displacing and imprisoning many more.