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Damian Victor Sargeant (31) was the first duty manager employed at Craft Bar & Kitchen (CBK) in the Octagon and immediately volunteered to become till administrator.
Owner John Macdonald said the defendant had experience with the state-of-the-art system so it made sense to put him in charge.
But, in January, he was contacted by the monitors of the cloud-based system.
They told Mr Macdonald someone had set up a hidden button, which allowed them to take cash from the till.
''[Sargeant] logged on to the till using his personalised code and proceeded to alter the till computer system to allow one of the keys to remove $100 from the night's takings when activated,'' the summary of facts said.
He used the function 13 times between November 18 last year and January 2.
Armed with the information about the fraudulent activity, Mr Macdonald summoned Sargeant to a meeting and informed him it was about ''financial irregularities''.
''I never saw him again,'' he said.
After repeatedly postponing the sit-down and spending some time on stress leave, Sargeant resigned from his job on January 14.
Mr Macdonald described the former employee as ''very very manipulative''.
Sargeant also persuaded three staff members to resign in protest and Mr Macdonald said some of them filed affidavits with the court on the defendant's behalf after he initially denied the allegations.
CBK was ''unbelievably busy'' over the summer period and the employer said it was very hard to find replacement workers then.
Sargeant eventually pleaded guilty to a charge of theft by a person in a special relationship but when he appeared before the Dunedin District Court yesterday his position was less clear.
He had told Probation he had only pleaded guilty to put an end to the proceedings.
Counsel Jim Takas called it an ''Alford plea'', something available in the United States legal system whereby someone can plead guilty without accepting criminal culpability.
Judge Kevin Phillips was unimpressed by the flip-flop but agreed to sentence the defendant despite his ''attitude and protestations''.
Sargeant got three months' community detention (to be served in Christchurch), 60 hours' community work and was ordered to repay the stolen $1300.
Mr Macdonald said the recompense was a peripheral factor.
''The money was not the issue. What I want to ensure is that he doesn't hold a duty-manager's certificate again,'' he said.
''People like this need to be held accountable otherwise they'll continue to do it and continue to get away with it.''