But he admitted he has faced some challenges from within the organisation and that results had been disappointing.
The Otago Rugby Football Union announced yesterday Mooney has decided to take up a job offer at his old club, Wests, in Brisbane and will be leaving Dunedin in November, when his two-year contract comes to an end.
Mooney said he had left of his own accord after the job offer came up in the past couple of weeks.
"It has definitely been my decision and I was not pushed.
The union had talked about some sort of role about developing players and doing some sort of coaching. A sort of a rugby director," he said.
"But we did not get too far down the track with that and this offer came up and I elected to take it.
"This is my choice to go and people should not read anything into it."
Mooney (46) said the new position involved development, coaching and a bit of marketing at a club where he had both played and coached.
Mooney's two years in charge of Otago did not meet with much success, with the team slumping in 2010 to two wins from 13 games for last place in the ITM Cup.
Otago improved this year to win half of its 10 games, and finish third in the Championship, or 10th overall of the 14 provinces.
Mooney was head coach last year but was appointed co-coach with Andy Hunter in the just completed season, following a full board review after the disastrous 2010 season.
Mooney, wife Steph and two children Tom (10) and Ben (8) will return to Brisbane where they still own a house.
He said looking back over the two years the highlights would have been defeating Auckland at Eden Park this year, Otago's first win on the ground for 35 years, and the development of young talent such as Gareth Evans, Hayden Parker and Liam Coltman.
He said the lows were obviously the performance of the team in 2010, and the challenges faced within the union. He declined to elaborate.
Many thought Mooney would be on the outer after the 2010 season but he stayed although assistant coach David Latta was not re-appointed.
It was just the nature of professional sport that other opportunities would come up and people would move on, Mooney said.
He did not nominate a successor, saying that was up to the board to decide.
ORFU general manager Richard Reid said it was sad to see a good person like Mooney move on but also said that was just the nature of professional sport.
Mooney had not been offered anything for next season and the review of last season would be discussed at a board meeting next Monday.
He confirmed Mooney had not been pushed but had simply taken up the new position in Brisbane.
Reid said it was hypothetical whether or not Mooney would have been offered a new contract for next season and what the season review recommended, as he was now moving on.
The union would move quickly to get a replacement coach and to determine the structure of the coaching positions.
He hoped to have a coach appointed by November, as pre-season training was under way well before Christmas.
