The approval by the Charity Commission marks the end of a long process of debate, appeal and evolution at the Plymouth Brethren.
The Charity Commission's initial refusal in 2012 led to an appeal which had to be temporarily halted because of legal fee issues, before eventually resulting in a decision in favour of the Church on Thursday.
The controversy rested on whether the trust's religious activities could be described as "advancement of religion for public benefit", part of the criteria for the Charity Commission's acceptance of religious organisations.
In official documentation on the subject, the Charity Commission states that in order for a religious organisation to be recognised as charitable, they have to demonstrate that their aims are for the public benefit.
"It would not be sufficient for any such organisation to show that it is established solely for the benefit of the followers or adherents of the religion," the guidance states.
In its decision document on the Plymouth Brethren, the Charity Commission outlined concerns about "the doctrine of separation from evil, which… resulted in (i) both a moral and physical separation from the wider community and (ii) limited interaction between the Brethren and the wider public".
This doctrine resulted in policies such as limiting the attendance of church services to those who were already considered members and forbidding members to socialise in any way with non-members.
The commission said it had received evidence relating to allegations of "detriment, harm or disbenefit" following its 2012 decision to refuse charitable status to the Plymouth Brethren.
Disciplinary procedures against members were found to include the controversial practice of "shutting up", where members of the congregation are not permitted to speak to a particular individual.
The possibility that this practice was inflicted upon children was investigated in early 2013 by Parliamentarians.
This practice had previously resulted in the physical separation of family members to such an extent that non-Brethren family members were not permitted to attend their Brethren relatives' funerals.
The decision document also claims of legal action against former members, and members who left the Church being "ostracised and consequently treated differently from other members of the public".
Dialogue between the Preston Down Trust and the Charity Commission resulted to changes to the trust's governing document and the Commission being satisfied that it met the requirements for charitable status.
It is uncommon for the Charity Commission to take such an approach, a fact that was remarked upon by Tory peer Baroness Berridge, who was involved in gathering evidence in relation to the Church.
"The grave concerns of the Charity Commission should not be underestimated as they have required the EB (Exclusive Brethren) to agree to a 'faith in practice' document and it is remarkable for them to require a religious group to, in effect, alter its practice and doctrine to qualify for charitable status," she said.
She also echoed concerns about the Plymouth Brethren's practices, saying: "This religion is not one I recognise as Christian."
The Plymouth Brethren welcomed the outcome in a statement that read: "This decision is a great relief to us and we are hugely encouraged and comforted, that after a thorough explanation of our Christian beliefs and practices, which are based on the infallible and eternal Word of God as set out in Holy Scripture, the Charity Commission has agreed that the doctrines and practices of our Church advance religion for the public benefit."
The decision to grant charitable status could still be appealed and the Charity Commission will be reviewing the status in a year's time.
Baroness Berridge added: "I recognise that those harmed by their experience of the EB may be disappointed by today's decision and may have relevant standing to appeal the decision."
Explaining its decision to grant charitable status, the Charity Commission said the trust had "demonstrated a willingness to make amends and to do what it could as a Christian organisation to ensure, as far as it was consistent with its religious beliefs, it would act with Christian compassion in the future".
Changes include ensuring worship services are open to all members of the public and making it public what the accepted dress code is to those who wish to attend.
In a section of the new governing documents entitled "Compassion", the trust sets out how that pastoral care should be provided "including but not limited to where fault occurs".
"No action should be taken in any way to treat vindictively, maliciously or unfairly persons whether within or outside the community, including those who were within the community and who are leaving or have left the community," it says.
"Every care should be taken to provide for and support the welfare and education of children and young persons within the community.
"Where persons seek to leave the community, reasonable assistance should be afforded to them in terms of support and/or financial assistance relating to employment or other matters, where they have been dependent on the community for that support."
The new governing document also states that "reasonable steps" should be taken to allow the continuation of family relationships when a family member leaves community, including providing access to family members, especially children.
The Plymouth Brethren Christian Church welcomed the Charity Commission's decision in a statement, despite noting that it did not agree with all aspects of its opinion.
Spokesperson for the Plymouth Brethren, Gerry Devenish, refused to be drawn on the specifics of what they disagreed with but told Christian Today that their core values "as a mainstream Christian church remain unchanged".
He said the Charity Commission's opinion document "speaks for itself" and was positive about the new governing document making the Church "more accountable".
William Shawcross, chair of the Charity Commission, was quoted on ThirdSector.co.uk as saying: "I am pleased that the PDT has agreed to adopt a new governing document and am confident that the organisation now qualifies for charitable status.
"This was a complex and sensitive case, which involved strong views and feelings on both sides of the argument. I am grateful to all those who shared information with us, and for their patience in awaiting today's decision.
"I hope that the organisation's new explicit focus on compassion and forgiveness will help allay the concerns of people who remain uncomfortable with some of the practices of the Plymouth Brethren Christian Church."