In March this year, the woman wrote to her union expressing unhappiness with some aspects of her new job.
At a meeting to address the issues, the woman's manager said she had taken five sick days in six weeks due to migraines, which the manager considered to be "extreme absenteeism".
She suggested the woman go for counselling which the company would pay for.
Annies' general manager Nicola Martin said she wanted a report from the woman's doctor to say she was fit for work, the finding said.
The next day the woman told her manager she was not happy, and made a fist.
The manager told her she would not be intimidated. The woman turned away and allegedly said "f*** your job".
The woman was then taken into the smoko room where she took a pair of scissors from a drawer and put them against her wrist. When she was told not to be silly she put the scissors back in the drawer.
The woman was suspended on full pay and sent home and a counselling session was arranged.
In May, the woman was sent a letter dismissing her on the grounds that Annies considered the March incident amounted to serious misconduct.
It concluded her "behaviour on that day was of a very serious kind and put you and others at risk".
However, ERA member Christine Hickey said the woman's behaviour was not sufficient to amount to serious misconduct, particularly as the swearing was not directed personally at the manager as an insult.
"I note too that there are no active warnings on (the woman's) file at all, let alone for similar behaviour."
Some of her co-workers told the ERA they were not comfortable with the woman returning to the company because she was "volatile and unpredictable".
But Ms Hickey said the threat of self-harm did not appear to be a serious attempt, and was easily resolved.
Justice favoured the woman to be reinstated after a doctor certified she was well enough to return to work, Ms Hickey said.
Annies' lawyer Mike Hardy-Jones said the company had not decided whether it would appeal against the decision.
The woman's lawyer Luke Radich said his client was looking forward to returning to work and renewing acquaintances with her old workmates.
"Her job is really important to her and she can't wait to get back."
Annies is best known for its dried fruit products which are sold throughout New Zealand and Australia and in parts of the USA.