The first 25 to 40 aviation students will be receiving lectures in those historic classrooms by mid January, New Zealand International Commercial Pilot Academy (NZICPA) chief executive Phill Bedford said.
They won't need the whole complex, and Whanganui's YMCA has a guarantee it can stay on for 18 months.
It will lease the space it needs - about 50 per cent of the total - from the new partnership.
The sale is "a sweet moment" for YMCA interim CEO Kevin Ross, who said Uncle John (Maihi) has often told him of former Māori settlement in the area.
"I do think that link is really important. It had the opportunity to be lost in a commercial enterprise," Ross said.
Ngā Tāngata Tiaki chairman Gerrard Albert said the purchase was the first investment the trust has made locally, and happens in the second year after full settlement of the Whanganui River Claim.
"It's great to be able to start that profile at home, and catch up with the Ngāti Apas and the others around the place."
The site could have other training uses in future, and he wanted the community to benefit economically.
"That underlines everything. We want to make sure the community is being served by the investment here."
The buildings on the site were owned by YMCA Central, and the land was leased from Whanganui District Council.
Apart from one hall, all the buildings have earthquake strength at least 33 per cent of a new building.
But they will have other challenges, Doyle said. The flight school will initially use lecture rooms and a breakout space and doesn't intend to accommodate students there.
It has outgrown student accommodation in the Dublin St Apartments, and by mid 2020 its students will fill the former Nazareth Rest Home, Bedford said.
Holdings chairwoman Annette Main liked that the sale and partnership cements the relationship between council and iwi, and that Mayor Hamish McDouall and the council had confidence in it.
Doyle said it was a rare opportunity to purchase at just the right time.
"In business it's not often that you have all the moves aligned."