After that, Judge June Jelas told the 12 jurors she would accept a majority decision.
The jury continued deliberations into the afternoon today.
Coronakes, 34, waived her right to automatic name suppression as the trial began last week.
Jurors heard Coronakes claimed Koning grew enraged, throwing food on the floor of his flat after she surprised him and a friend by turning up with a home-cooked meal.
The Crown alleged Koning then raped her in the same flat 16 years ago.
"Looking back, I feel like a bit of an idiot for having a go at her bringing food over," Koning said last week as he gave evidence in his own defence.
"I wouldn't say I mistreated her. I would say it was a bit of an overreaction," he added.
But at the trial, Koning denied rape, and rejected suggestions he used the threat of suicide to persuade Coronakes to keep quiet after the sexual assault.
'Amy was telling the truth'
Outisde court, Coronakes' mother Glenis Parker said she was incredibly proud of her daughter.
"Amy was telling the truth, and they believed her. I'm just proud of Amy coming forward and telling the truth.
"This case was about Amy."
Coronakes now lives in Australia but was aware of the verdicts within a few moments of the jury's decisions.
Parker said the prosecution and trial process was the most difficult experience she'd ever encountered.
The guilty verdicts mean Koning's past and profession can now be reported.
On his LinkedIn page, he described himself as having a background in DJ'ing, event and party planning, and sailing.
He established the Floating Foundation, a charity he said met the needs of remote communities.
In 2018, allegations of Koning behaving inappropriately towards multiple women who worked with him surfaced.
Allegations he was quick to anger were frequently raised at his trial.
But jurors were not told of the earlier reports about Koning's role in the Floating Foundation.
In 2018, Koning admitted to treating women poorly and behaving inappropriately.
In an interview with the Sunday Star-Times, he admitted to excessive drinking and said he had to change.
Koning was silent and expressionless as the verdicts were announced on Tuesday afternoon.
A sentencing date was not established but Judge Jelas told Koning he would be sentenced probably in the new year.
Where to get help:
• If it's an emergency and you feel that you or someone else is at risk, call 111.
• If you've ever experienced sexual assault or abuse and need to talk to someone call the confidential crisis helpline Safe to Talk on: 0800 044 334 or text 4334. (available 24/7)
• Male Survivors Aotearoa offers a range of confidential support at centres across New Zealand - find your closest one here.
• Mosaic - Tiaki Tangata: 0800 94 22 94 (available 11am - 8pm)
• Alternatively contact your local police station
• If you have been abused, remember it's not your fault.