Reverend Tom Poata, The Right Reverend Ngārahu Kātene, Bishop of Te Manawa o Te Wheke and Wally Tangohau, parish council chairman greeted them inside.
Amid the hush of the more than 1000 welcomers, those in front of the meeting house are saying a traditional chant.
Poata will show them around the church noting, in particular, the iconic Galilee Chapel window.
The remainder of the royal entourage has remained outside the church.
The royal couple have been introduced to Robert Gillies, the last surviving member of "B" Company in the 28th Māori Battalion and Bryce Morrison, Rotorua RSA president.
Prince Harry is having a long conversation with Gillies, 93, who has spent the last week helping prepare the marae.
The couple are both wearing large greenstone necklaces.
Korowai have been placed on the shoulders of the royal couple by Kahurangi Milne and Ana Morrison.
The couple are now preparing for the pōwhiri where they will be accompanied by Maxwell, Milne and Morrison.
The first warrior, Taiwera Kautai, is approaching the royal couple, with a taiaha in hand, acting as the scout.
When the Queen came in 1953 they didn't know her dimensions so Te Arawa made two identical cloaks, a small and a medium. She ended up being a small and so the medium is the one on display today.
Those who weren't invited inside the wharenui are now making the most of the sunshine, watching the speeches inside on a large screen.
Rotorua has given the royals a rousing welcome. Kaumātua Monty Morrison is now speaking to the royal couple inside.
Council cultural ambassador and district councillor Trevor Maxwell is sitting next next to Prince Harry and is translating for the prince.
There are three speakers including Monty Morrison speaking on behalf of Te Arawa, Professor Piri Sciascia and speaking on behalf of the royal party and Te Kanawa Pitiroi speaking on behalf of Ngāti Tuwharetoa paramount chief Sir Tumu Te Heuheu.
Te Arawa is now giving a hongi to their guests and they will soon leave the meeting house before walking into the neighbouring wharekai for lunch.
These have been created by Living Colour and include Lily of the Valley flowers which were in Meghan's bridal bouquet. These only bloom for two weeks each year and it happens they actually bloomed last week.
Rotorua mayor Steve Chadwick is now giving the last speech on behalf of the Rotorua community.
"Rotorua is a very unique and special place in the world and this place Te Papaiouru marae especially so."
She said when previous royal tours had come to Rotorua they had been shown it is the heartland of Māori culture.
"As you visit now, in 2018, you can be assured that is still the case.
"As our confidence as bilingual district grows, so does our confidence in our people and our future."
As the couple left she said haere mai and welcomed them to Rotorua
"Its been a really wonderful experience today," she said. Harry gave her a hongi and kissed her friend Margatet Jenkins, who also helped in the kitchen, on the cheek.
Before eating, the couple also met Karena and Kasey Bird, 2014 MasterChef winners, who prepared the menu.
Following a prayer they ate with 180 invited guests and with entertainment by Ngāti Whakaue Senior Kapa Haka, Promise Royal, Hohaia MacFarlane, Lizzie Marvelly, Turanga Merito and Raukura Kapa Haka.
The royal couple have now moved from lunch into Te Ao Marama.
They were accompanied my Kuia Norma sturley and waved at the school children who were still outside.
Inside the Te Ao Marama Church Hall they met young Te Arawa people involved in mental wellness in the community, university students achieving in professions where Māori are under-represented (architecture, dentistry, engineering), students involved in Māori language revitalisation and young Māori creating in the e/digi space.
Outside some of the kapa haka performers took the opportunity to pose for photographs with the police motorbikes for the motorcade.
Member of the Ngāti Whakaue Senior Kapa Haka roopu Lauren James said it was a real privilege for them to perform during the luncheon.
"We represent not only this marae but the people of this land."
She said the royal couple looked like they had enjoyed the performance.
"What we've seen today is a couple who are willing to engage with and learn about different cultures.
"To have a royal couple like that come here, its very exciting and we couldn't have asked for a more picturesque venue here beside the lake and with such amazing weather."
Rotorua Primary School teacher Missy Te Kiri said two kete had been gifted to the Duke and Duchess.
The two kete had been made specifically in the school colours.
"One had set of poi in it, that was in the school colours too and in the other we had a full set of Aunty Bea's books."
The whole school had come to Te Papaiouru today for the visit, more than 200 pupils.
Pupil Kaihau Pou Poasa, 12, said it had been "amazing".
Earlier at the airport, there were about 300 people pressed against the airport fence waiting to catch a glimpse of the couple.
A group from a local kohanga reo has brought 14 children to the airport hoping to catch a glimpse.
Rotokawa School principal Briar Stewart said she had brought the school down to the import to create memories.
"It's such an opportunity for great memories for children. A lot of us have had times we've gone to a place with our schools. For me it was manukau city for Charles and Diana so we're creating an opportunity for the kids.
"We're the school across the road and we hear the planes come in all the time."
Rotorua local Madeline Lauder has been waiting since 9.30am.
Meanwhile at Ohinemutu, Te Arawa are warming their voices with a powhiri run through.
Local Māori are preparing to welcome royalty to the traditional Māori geothermal village of Ohinemutu, on the shores of Lake Rotorua.
At Ohinemutu security are seen on street corners and those involved in the welcome are starting to park and make their way to Te Pāpaioūru Marae.
Three bus loads of international media have arrived at Ohinemutu where they, along with local media, will have their own pōwhiri at Tunohopu Marae, 50m away from the main marae.
The mood among international media is that Rotorua has "stolen the show" with its welcome. One cameraman said "they have saved the best for last".
The Sun royal correspondent Emily Andrews from London said it was the first time in the whole tour the media had been welcomed especially.
"Rotorua has given us such an amazing welcome it was so lovely to have a formal welcome ceremony. To be personally welcomed and given food, which is is incredibly kind and touching, has made us feel fantastic. We love Rotorua."
Sky News cameraman Adam Cole said Te Arawa's welcome gave him goosebumps.
"This is spectacular ... It's a hell of a way to end the tour. That ceremony was so powerful."
Cole said the royal couple were also welcomed at Government House with a powhiri.
"This trumped it. The whole press pen said the same thing. And yes I did think it stole the show, what a great last day."
Eager royalists are already gathering at the Government Gardens, ensuring they secure a prime spot to see the Duke and Duchess during their 3.30pm walk.
Christchurch woman Angie Hira, originally from Rotorua, decided at the beginning of the royal couple's tour she would come up to Rotorua to try meet Prince Harry.
"I contemplated staying the night just to make sure I got a good spot! I was expecting it to be packed already.
"I've loved the royals since I was 10. I would love to meet Harry today and have a bit of a korero.
"I would tell him I admire his tenacity and my whānau have been praying for him and his family.
Hira said she would pass the time by chatting with locals.
Meanwhile, suspense is building at a treewalk park in Rotorua ahead of Prince Harry and Meghan's anticipated visit this afternoon.
The walk through the Redwoods Treewalk, a 700m-long walkway of suspension bridges between 117-year-old redwood trees is expected to be one of the highlights of a very busy day in the Bay of Plenty.
Redwoods Treewalk co-founder Bruce Thomasen told NewstalkZB it's a glorious day in Rotorua, with not a cloud in the sky.
"We've got a lovely suspended bridge system through the redwood trees. We'll put them through this canopy of beautiful forest and talk to them about the local stories.
"They will be with us a short amount of time, only 20 minutes with us."
Thomasen said it had been a whirlwind putting together the plans for the visit as the forest trust only received confirmation when a press release was issued with the itinerary for the royal tour.
"The treewalk team are excited and my phone is going hot with 'good luck' and 'congratulations'."