Members voted over the weekend to revoke the Church's constitution.
It means its National Leadership Team will step down from roles once the winding up has been completed. The independent congregations will then appoint their own leaders who will be responsible for finance, staffing, and safeguarding.
The Church blamed a badly damaged reputation, declining membership and a slowdown in giving for the closure.
In a statement posted on the Church website, an apology was given for the "faults and failures" which have had a profound impact on many people's lives.
It said: "We are deeply sorry for, and appalled by the abuse that has taken place within Jesus Fellowship Church and the New Creation Christian Community (NCCC) and offer our heartfelt sympathy and unreserved apology to all those affected.
"Children and vulnerable people were entitled to expect full protection from harm. We acknowledge the pain many of those people continue to feel. As things have become clearer to us, we are grieved and deeply troubled."
Back in 2013, the Church invited members to come forward with personal experiences with many making disclosures of pastoral abuse and bullying as well as financial, physical and sexual abuse.
Historic allegations were passed on to police and a number of prosecutions were brought.
The Church has been working with Christian safeguarding charity Thirtyone:Eight over the past couple of years to address past wrongs.
Chief executive Justin Humphreys said: "With news of the closure of Jesus Fellowship, it's important that the offences committed continue to be acknowledged and that survivors are properly supported in their attempts to seek justice.
"Therefore, we remain committed to offering our support to Jesus Fellowship so that they may continue to implement robust safeguarding measures as they transition to independent congregations, and that all the valuable learning gained from this process may be retained and built upon so that the individual churches may create safer places for all."
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