Earlier in the week a white gunman shot nine black members to death during a Bible study group at Emanuel AME Church.
On Friday 21-year-old Dylann Roof was charged with nine counts of murder and possession of a firearm, according to Charleston police.
Pastor Revd Clementa Pinckney was amongst those killed.
Emanuel AME announced services and Sunday school would be going ahead as normal.
Temporary pastor Revd Norvel Goff said: "The devil also entered - and the devil was trying to take charge.
"Thanks be to God, hallelujah, that the devil cannot take control of your people. And the devil cannot take control of your church."
Similar sermons of recovery and healing were heard throughout the country.
A show of solidarity was planned throughout the city, with church bells ringing in unison.
Harold Washington, 75, said it would host even more newcomers: "We're gonna have people come by that we've never seen before and will probably never see again, and that's OK.
"It's a church of the Lord, you don't turn nobody down."
During a special service outside the church over the weekend, a multiracial women's group sung Amazing Grace.
Shae Edros, 29, from the group said: "I think just because of what people have gone through emotions are definitely heightened, not just in Charleston but with anyone going to church because it is such a sacred place, it is such a safe place."
"To have something like that completely shattered by such evil - I think it will be in the back of everyone's heads, really,"
Revd Ed Kosak from Unity Church of Charleston said delivering Sunday morning's sermon would be emotionally taxing but he felt empowered by the strength and grace Emanuel African Methodist Church members had shown.