Fire officials suspect a chemical used to clean some of the chocolate-making instruments became part of a chemical reaction.
The worker who died had not been identified by police as of Sunday evening.
"They were mixing their chocolates. They were using these pellets. It was a by-product that gave off an ammonia smell. High heat was in the building and [it] overcame the workers," said Chicago Fire Dept. Deputy Chief Anthony King.
The fire department said later Sunday that the factory was safe again.
The Chicago Department of Health said it would have inspectors inside the factory early Monday morning.
A Blommer spokesperson was not expected to comment until Monday.