Amanda Zilliken took to Facebook to air her grievances and said the church should be ashamed.
Zilliken explained that she attends the megachurch every Sunday and said she's never had a problem breastfeeding in the church until the recent incident.
The post got more than 1,600 shares and several commenters sympathised with the mother.
According to North Carolina, breastfeeding is allowed anywhere in public.
Women who saw the mother's post have taken her side and planned a 'nurse in' at Elevation on 20th August.
The Facebook event group details read: "Amanda was asked to leave in the middle of church and escorted to the bathroom to continue nursing her baby "for the comfort of others". Let's come together and have a Nurse-In to support Amanda!"
Elevation Church, led by Pastor Steven Furtick, released a statement to local Charlotte, North Carolina TV station WSOC-TV.
The church said breastfeeding mums have always been welcome to stay in the sanctuary and apologised for any offence caused.
The statement reads: "We do not have a policy that nursing mothers can't be in the sanctuary.
"A volunteer had a conversation and felt both parties arrived at the same conclusion to exit mutually. We are sorry that this in any way offended anyone. We welcome everyone and anyone to attend Elevation church.
"We have several designated areas for nursing moms at Ballantyne specifically- one private to allow pumping and it's close to the auditorium for convenience and the other in the actual baby area with a TV to allow mothers to still be part of the worship experience."
Elevation, which is one of the fastest growing churches in the US, also told WSOC-TV that it offers child care during services and it has several designated areas for nursing mums if they opt to use them.