Federal regulators stopped operations at Sunland Inc.'s New Mexico plant, using new enforcement authority gained with the 2011 food safety law.
Investigators found salmonella throughout the plant after 41 people in 20 states were sickened by peanut butter sold at the Trader Joe's grocery chain.
Sunland had voluntarily closed its peanut processing facility after the September outbreak, and it had planned to reopen this week. A Sunland spokesperson said the FDA's decision to suspend the registration was a surprise to the company.
Before the food safety law was enacted, the FDA would have had to go to court to suspend a company's registration. The company now has the right to a hearing and must prove to the agency that its facilities are clean enough to reopen.
Sunland is the nation's largest organic peanut butter processor and sold hundreds of products to many of the country's largest grocery chains, including Target, Safeway and Whole Foods.
The Associated Press contributed to this report.