The mission has been granted consent for the project, something general manager Laura Black said she was very happy with: "And you can quote me on that."
Construction, though, was "a long, long way away", with $4 million of the cost still to be raised.
A resource consent hearing in March considered the mission's plan to demolish the church and replace it with the social services complex.
The hearing became an argument between heritage advocates, many of whom wanted the 1894 church building saved, and the mission, which wanted to demolish it to build a facility it said would be far more suitable for the mission's purpose.
Evidence was the mission could legally demolish the building without consent, and that the church was protected neither by New Zealand Historic Places Trust listing, nor the council's district plan.
While the mission argued there was a real need for its planned complex in one of New Zealand's poorer areas, the New Zealand Historic Places Trust said options for retention, sale or adaptive reuse of the building had not been pursued.
The hearings committee, of Dunedin councillors Colin Weatherall, Richard Walls, and Andrew Noone, said in its decision the project itself had received support from many, and had been specifically opposed by none.
It recognised the application was for the construction of the complex, "not for the demolition of the existing buildings on-site".
"In this case, the permitted baseline allows for the clearance of the site, as a resource consent is not required to remove any of the existing buildings."
Declining consent would not guarantee the building would be saved.
Dealing with the trust's opposition, the committee noted the trust did not have a representative attending "for the great majority of the hearing", and missed nearly all the applicant's presentation.
Other opposing submitters had directed their concerns at the wrong forum, as the committee could not declare the building protected, could not vary the council's district plan, and did not administer a heritage fund.
Ms Black said there would be intensive activity in the next 18 months to two years to raise funds for the project.
The mission was discussing the matter with various businesses, philanthropic trusts and other services locally and nationally.
The consent was a early step, necessary to show the mission could build on the site, and that it was serious in its intent.
The consent had a time limit of five years, and the project would be completed before that time was up, Ms Black said.
The New Zealand Historic Places Trust said in a press release it accepted the decision.
