Conroy's, a maker of smallgoods, has been charged with six hygiene breaches at its Bowden plant.
The Department of Primary Industries and Resources South Australia made investigations in February that found issues including with hand washing facilities, storage and pest control.
The ABC reports that the department issued Conroy's accreditation in 2009, requiring the company to adhere to hygiene standards.
No plea was entered yesterday at a hearing at Adelaide Magistrates Court, with the case to return to the court in March.
Conroy's had been the subject of a listeria scare in 2005, settling with the family of a man who died after a hospital served him chicken produced by the company.