The University's Director of Athletics, Bill Peterson, announced Carter's resignation Monday morning.
Carter will become the assistant coach at her alma mater, NCAA Div. II University of Alabama-Huntsville, effective immediately.
"I want to thank Shorter University President Dr. Harold Newman, Chairman of the Board of Trustees Dr. Nelson Price, Coach Peterson, Ricci Lattanzi and Vic Mitchell for the wonderful experience I had at Shorter," said Carter, who also cited Shorter head baseball coach Matt Larry and assistant coach Al Thomas as instrumental to her success on the Hill.
"For Shorter to hire me at a time when I had limited coaching experience and for those people to support me the way that they did over the past four years means so much, and our team would not have had the success that it did without that support," Carter said. "We built a successful program and we had a great group of girls. My career at Shorter wasn't just about winning softball games, but also the great things we were able to accomplish off the field and in the community. I feel like I grew as a coach and a person during my time at Shorter and I will always cherish my experience.
"Going back to UAH is something that I've always wanted to do. Even though this is another opportunity for me, this truly was the hardest decision I've ever had to make."
"We will definitely miss Coach Carter, both personally and professionally," Peterson said. "She has done an unbelievable job with our program and has put us in a position where we are now a national contender year in and year out.
"At the same time, we understand what happens when 'mama calls.' She just couldn't pass up this opportunity."
Former Lady Hawks' head coach Al Thomas, who had served as an assistant with the Shorter softball program during Carter's tenure as head coach, has been named Carter's successor.
Thomas' resume includes nine years of collegiate coaching experience. He led the Lady Hawks' to the program's first-ever winning season in 2006.
Thomas also spent 20 years with several Major League Baseball teams in their scouting and player development departments.
"Al has worked hand-in-hand with Melanie to help build our program from the ground up," Peterson said. "He has been instrumental in recruiting most of our kids and we are extremely confident that he will continue to move our program forward.
"We could not be more pleased with Al's selection and we look forward to another big year this spring."
"I am excited about the opportunity," said Thomas, who along with the aforementioned Ricci Lattanzi led the Lady Hawks to 24 wins in 2006, 19 more than the previous season. "We have a great thing going so we are going to keep things business as usual and not make too many changes."
Shorter introduced fast-pitch softball as a varsity sport in 2004, but it was Carter's arrival in 2007 that sparked the program's rise into national prominence.
Carter was named the Southern States Athletic Conference and Region XIII Coach of the Year in her rookie season with Lady Hawks in 2007, a season that began a run of three straight SSAC titles - a regular season championship in 2007, both the regular season and tournament titles in 2008 and a tournament crown in 2009.
In Carter's four seasons with the Lady Hawks, her teams made four consecutive appearances in the NAIA Softball National Championship, including a program-best fifth place finish this past season.
Shorter compiled three 50-win seasons under Carter's leadership - the only 50-win seasons in program history - including a school record 51 victories in 2010. Carter leaves Shorter with 195 career head coaching victories.
She departs to an Alabama-Huntsville program for which she established herself as one of the best players in the school's history from 2000-2003. Named to the Gulf South Conference All-Decade Team one week ago, Carter, a four-year All-American, still holds Gulf South and UAH records for career runs (231), RBI (233) and doubles (65).
Though Carter's resume is impressive, Thomas has served as the architect of the Lady Hawks' four successive championship teams.
Thomas was instrumental in the recruitment of all six of Shorter's All-Americans over the last five years, including three-time All-America pitcher and infielder Libby Munson, who has served as an anchor for the Lady Hawks' pitching staff in her first three seasons with a career 78-17 record, 1.29 earned run average and 631 strikeouts in 111 appearances.
Thomas' 2010 senior class of All-Americans Tiffany Adams and Dandi Ammons as well as All-SSAC selections Elisabeth Barber and Hannah Strength and key contributor Liz Clark, will go down as arguably the most talented and decorated senior class the program has ever had.
Thomas is more than confident that the Lady Hawks' gifted group of returners coupled with a blue chip recruiting class of eight athletes will keep Shorter atop the SSAC ranks for years to come.
"It will be tough to replace the caliber of play and leadership qualities of that  class, but we tried to bring in some players that could step right in and plug those holes with depth," Thomas said. "We addressed the leadership with some talented JUCO transfers and the freshmen coming in are a mixed bag of speed, athleticism and power.
"Anytime you can add all of those dimensions to your team, it is beneficial."