A High Court jury has begun deliberating the fate of a respected Auckland businessman accused of stealing $1.3m from a rest home.

The man, who has name suppression, faces 49 dishonesty charges linked to alleged offending spanning seven years.

The Crown argues he overpaid himself and his wife, and fraudulently used 1100 cheques to siphon money from the business, with much of the money being paid to contractors working on the couple's dream house.

The man was employed alongside his wife to run the aged-care facility from 2001 until 2012 and was responsible for overseeing the payroll, paying suppliers and the company's financial records.

He is on trial in the High Court at Auckland before Justice Timothy Brewer.

The jury retired just after 3pm today to begin considering their verdicts.

On Friday during closing arguments, Crown prosecutor Sam McMullan argued the man established a system of codes and concealment, intermingling his personal and company funds in a way that enabled him to take money when he needed it.

Justice Timothy Brewer is presiding over the case in the High Court at Auckland. Photo / NZME

"He created the system so he could exploit it."

The amounts he took increased as his spending went up when he was building a new home, the prosecutor said.

"His credit cards were completely maxed out, paying for his house really stressed their accounts," the prosecutor said.

When the cards came tumbling down in 2012, the man allegedly took boxes of records from the rest home basement - evidence of what he'd done over the years - and destroyed them, McMullan said.

Over two days of cross examination, the man said he did not know in response to most of the prosecutor's questions about specific expenses.

"But did he really not know?" McMullan asked. "The way he paid his and his wife's salaries over the years. Is it true he could not recall?

"Put his evidence to one side. It's not worth anything."

Defence lawyer Fletcher Pilditch says the man's finances were chaotic but this does not make him a criminal. Photo / NZPA

Defence lawyer Fletcher Pilditch argued the jury could not be sure beyond reasonable doubt that the man was dishonest and took money without claim of right.

Pilditch said the problem with the Crown case was they assumed fraud and worked backwards, but the prosecution couldn't prove the money wasn't spent on the rest home or authorised reimbursements.

On salaries - the business partners had an "organic" relationship based on meetings and coffees and didn't have records of what was agreed upon.

Pilditch said the jury shouldn't believe the version of events put forward by the company director because he was out to "blacken" the defendant's character.

It was implausible that the couple would have worked for years at the rest home with no or such low salary increments, Pilditch said.

The man was "not great at accounting" and his finances became intermingled with that of the rest home.

"It looks like a bit of a shambles, because it was," Pilditch said.

But he argued that poor practice and poor management was not a crime.

"His failure doesn't make him a criminal."

Summing up this morning, Justice Brewer said the jury must decide their verdicts solely on the evidence put before the court, and make decisions on people's credibility and reliability.

He said the Crown case was that the defendant was dishonest and "used the rest home's money as though it was his".

"But the Crown doesn't have all the rest home's records. They went missing. The Crown wants you ... to draw the inference that he was dishonest.

"The Crown case is that it all came crashing down because so much money was being taken ... that the IRD wasn't paid, and if there's someone who's going to notice not being paid, it's the IRD."

However, the defence case was that the man was entitled to the money to reimburse him for legitimate rest home expenses, or that the money had been paid for goods and services such as gym memberships and Sky TV subscriptions that had been agreed as part of his employment package.

The defence case was that the documents presented to court as evidence against the man did not prove what the Crown contended and the case was "built on a foundation of sand", the judge said.

"The defence says there has never been an independent investigation into these allegations.

"[The man] denies he had anything to do with removal of documents from the rest home.

"He says all payments were legitimate expenses for the rest home or legitimate reimbursements due to him."