Chipotle Mexican Grill is undergoing structural changes after a string of E. coli outbreaks at stores nationwide created a public relations nightmare, changing up its cooking methods in order to safeguard against contaminated ingredients.

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According to the Associated Press, a number of food preparation protocols are being altered to block against potential bacteria. That means measures like dipping onions in boiling water before being chopped, marinating raw chicken in sealable bags instead of bowls, and strategically combining preparation methods already in place, such as adding cilantro to hot, freshly cooked rice, or mixing some ingredients with citrus juice to kill microbes.

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Preparatory work, such as chopping some ingredients, shredding cheese, and testing meat samples before shipments are bagged and sent to stores will be done in centralized locations in order to streamline testing and ensure sanitary conditions.Many of the new safety measures will be rolled out in the coming weeks.

"When you're given a project like this, you look at the universe of hazards," Mansour Samadpour, CEO of a laboratory firm hired to help the company with safety procedures, told the AP.

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Chipotle has had a series of recent public relations gaffes, with dozens of customers falling ill after eating at their restaurants.Earlier this week, the Centers for Disease Control and Prevention announced they would launch an investigation after five people were found with E. coli after eating at Chipotle restaurants in Kansas, North Dakota, and Oklahoma. In October, 43 Chipotle restaurants were shut down in Oregon and Washington after E. coli cases were traced to those states. Other cases were later reported in seven other states, and more than 140 Boston College students fell ill after an unrelated norovirus outbreak in November.

Investigations have not yet traced the bacteria to any particular ingredient, but Chipotle's approach, which lauds freshly prepared produce and meats, could make its food more prone to contamination. The company hopes the new measures will close loopholes without sacrificing its brand.

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"If I'm eating a burrito that had tomatoes that were chopped in a central kitchen in the salsa or one that was chopped in house, I probably couldn't tell the difference," founder and CEO Steve Ells told CNBC last week.

In the meantime, Chipotle took a financial hit this week after its stock sunk Tuesday following the news of the most recent E. coli outbreak.