Sen. Chris McDaniel (R), one of the most vocal opponents of the measure, described attempts to change it as part of an effort to challenge the founding values of the country, warning that the American flag was next.
"It is a big step, however, in the journey we are on to recognise everybody's God-given humanity and self-worth", he said.
The bill would also establish a commission to redesign the ms state flag.
The Magnolia State is about to abandon its 126-year-old flag, which prominently features the Confederate battle flag, under the latest wave of public pressure. Gov. Tate Reeves said Saturday that he would sign a bill if it reaches his desk.
He had previously said that he would not veto a bill, but did not publicly back it.
Democratic state Senator Derrick Simmons of Greenville, who is African American, said the state deserves a flag to make all people proud. The new flag design will be decided by voters in the November election and the current flag will not be an option, however the new design will be required to include "In God We Trust".
This came hours after the lower chamber passed the bill, which would establish a commission to create a new design for the flag.
Four days earlier, SEC commissioner Greg Sankey had announced plans to pull any championship events from the state if the flag wasn't changed. If voters reject the design, the commission will offer another redesigned flag during the 2021 legislative session. For quite a while, I saw the flag as a symbol of Southern pride, associating it more with Lynyrd Skynyrd than with slavery. If you're frustrated, I'd encourage you to think of what today means to a rising generation of Mississippians. "I would guess that a lot don't even see that flag in the right corner up there", Edward Blackman, an African-American Democratic lawmaker, told colleagues during the debate Saturday.
"There's some of us who notice it every time we walk in here, and it's not a good feeling", he added.
This flag will soon be changing.
Republican John Faulkner congratulates Senator Briggs Hopson after the Senate voted to change the MS state flag.
Athletic directors and coaches from MS universities have also urged lawmakers to act.
"I understand many view the current flag as a symbol of heritage and Southern pride", country music star Faith Hill, a MS native, tweeted.
Former Mississippi Governor William Winter, who is now 97, served on then-President Bill Clinton's national advisory board on race in the 1990s and was chairman of the Mississippi flag commission in 2000.