Philippe Gletty was the boss of PVC and aluminium frame company, Princeps Alu, in the southern town of Doizieux.
He was shot three times in a crime that initially baffled police, until his long-time secretary, Bettina Beau, came forward to confess to the murder.
The lawyer acting for 41-year-old Beau said the crime was "linked to stress", reported newspaper Le Progrès.
Her lawyer denied that there had been any romantic relationship between the two.
Beau, who is married, had worked at the 50-person company since it was created in 2001.
"Her declaration was corroborated by technical elements gathered by investigators," the local prosecutor said.
Gletty disappeared on February 27th and the alarm was raised after his car was found abandoned.
A week passed before the body of the married father of two was found on March 4th, under a bridge.
According to regional newspaper Le Progrès, colleagues were still coming to terms with the double shock of their boss's murder and the fact his closest confidante was the culprit.
"We are all in shock," said the company's marketing director, Virigine Fontanel. "The news of his murder was already bad enough, but to find out it was her…We could have suspected lots of people, but her, never."
"They knew each other for 16 years. She was with him from the time the company was created in 2001," she added.
As for the motive of stress, "nobody believes it," she said.
"We all get stressed by our jobs, but it's not a reason to kill someone," said Fontanel. "The police will need to find something else to convince me."
Fontanel also discounted any talk of a romantic relationship or something money-related.
For the time being, the priority of the remaining employees is to keep the company going.
"There's work to do," she said. "Everyone is determined to keep the company going."