SDLP youth, women and LGBT + chairpersons resigned after the party voted on a partnership with Fianna Fail.
In a statement, Matthew Corr (youth), Caoimhe McNeill (women) and Matthew Carson (LGBT +) said they had opted for "the only way" of "procedural abuses" at the party's special conference in Newry on Saturday.
The trio remain party members, but Mr. Corr hopes that the SDLP leadership will heal the divisions caused by the vote.
SDLP's former city council in Belfast, Niall Kelly, also resigned after 14 years of thinking that the vote "would inevitably lead to a merger of the two parties."
He said that the "close deal that excludes Fine Gael and Labor is a regression".
The partnership between the parties was adopted by 121 votes to 53, with 53 voting for a broader partnership with Fine Gael, Fianna Fail and Labor.
The connection was rejected by a number of high-profile personalities in the SDLP, including MLA Claire Hanna from South Belfast.
Former party leader Alasdair McDonnell did not attend the special conference, instead spending his Saturday launching Fine Gael Youth in Belfast.
In their statement, Mr Carson, Mr Corr and Mrs McNeill raised a number of complaints and said that they felt that the conference was not conducted in the right way.
The trio claimed that the delegate information was not shared beyond the SDLP leadership "to prevent election campaigns or persuasions from being conducted for those who did not support the leader's position."
They said that the conference had been convened without the required notice period and that information about the partnership would be sent out the day before the vote.
"This is not a proper order, so we are doing things in SDLP now," the statement said.
Despite their feelings, the group said they would continue to campaign for SDLP candidates in the upcoming local elections, but warned that "party members will not be treated without consequences."
In a statement made after the vote on Saturday, the SDLP leadership confirmed that not everyone would be satisfied with the outcome.
"This partnership builds on the genuine desire to reach out to people across Ireland, driven by the desire to restore power to local politicians and change the lives of people who have been too long abandoned by our policies here . " the statement said.
"For some members, this decision was not their desired outcome, and the leadership recognizes this and is sensitive, and we will reach all areas of our party over the coming weeks and months to ensure that we move forward together."
Belfast Telegraph Digital