Salmonella in Bakery Products – Why Contamination is Rising

For decades, bakery products have been considered one of the safest food categories. Flour, sugar, butter, and eggs—while prone to certain quality concerns—were not typically seen as high-risk for Salmonella contamination. After all, doesn't baking temperatures kill harmful bacteria?

Yet, something has changed. Over the past few years, reports of Salmonella in baked goods have increased, prompting regulatory crackdowns, product recalls, and tighter inspections. The latest government data shows a consistent rise in contamination cases, with the United States, Poland, and India emerging as key hotspots.

What’s driving this trend? And more importantly, how is it going unnoticed until products reach the market?

A Growing Trend: Why Salmonella in Baked Goods Is On the Rise

According to recent reports from regulatory bodies, incidents of Salmonella in bakery products have been climbing since 2020. While the numbers fluctuate, the overall trend is upwards, with noticeable spikes in the last two years.

The data points to two key drivers behind this surge:

1. Worsening supply chain conditions and ingredient contamination
2. Increased regulatory scrutiny and more inspections revealing hidden issues

One of the most striking trends is that Salmonella-related incidents in baked goods are no longer just about flour and eggs. Today, regulators are identifying post-baking contamination, facility hygiene failures, and improper ingredient storage as equally significant contributors.

This insight has been timely identified and is available to users through the SGS Digicomply Food Safety Intelligence Hub. Feel free to explore the Food Safety Intelligence Hub demo and try this tool in action.

Global Impact: Where Are the Incidents Happening?

While the United States has the highest number of recorded incidents, this is a global problem.

• Poland and India have seen increasing regulatory actions, particularly for large-scale commercial bakeries exporting products internationally.
• Germany, Canada, and Australia have all reported cases linked to contaminated raw materials, highlighting the need for better ingredient sourcing.
• China and New Zealand have experienced sporadic outbreaks, but with less regulatory transparency, the true extent of the issue is unclear.

This geographic spread underscores the fact that Salmonella in bakery products is not just a localized issue—it's an international food safety challenge.

This insight has been timely identified and is available to users through the SGS Digicomply Food Safety Intelligence Hub. Feel free to explore the Food Safety Intelligence Hub demo and try this tool in action.

The Silent Culprits: How Is Salmonella Getting into Bakery Products?

Most consumers assume that once food is baked, it’s safe. And in theory, that should be true—heat kills bacteria. But when we take a closer look at the entire bakery production chain, it becomes clear that contamination risks don’t end in the oven.

Flour: A Hidden Reservoir of Bacteria

Flour is one of the most unexpected carriers of Salmonella. Unlike eggs or raw meat, flour doesn’t feel "perishable" or "risky." It’s dry, shelf-stable, and used in almost every bakery product. But that’s precisely the problem.

Flour is a raw agricultural product, meaning it can easily pick up pathogens during harvesting, transportation, or storage. Because flour isn’t heat-treated before being sold, any bacteria present survive until the consumer uses it.

Recent studies have shown that Salmonella can persist in flour for months, and if manufacturers don’t treat it before use, it becomes a direct contamination source for baked goods.

Egg-Based Fillings and Toppings: A Post-Baking Risk

Another major issue lies in post-baking handling—specifically, creams, custards, and other dairy-based fillings that are added after the product has been baked.

Many bakery products, from eclairs to cream pies, require the use of unbaked or lightly heated dairy-based components. If these ingredients are not properly pasteurized, they can introduce live bacteria into an otherwise safe product.

This is what happened in several recent FDA warning letters, where bakeries were cited for:

• Failing to use pasteurized eggs in custard-based products.
• Storing dairy-based fillings at unsafe temperatures.
• Not testing final products for bacterial presence before distribution.

Simply put, a contaminated batch of filling is all it takes to turn a safe pastry into a foodborne illness outbreak.

Post-Baking Contamination: A Facility-Level Problem

While raw ingredients are a significant risk, they’re not the only issue. Investigations into multiple bakery facilities have uncovered severe sanitation failures, including:

• Unclean storage areas, where rodents and insects come into contact with ingredients.
• Lack of proper handwashing and food handling practices among employees.
• Contaminated equipment, particularly cooling racks and slicing machines.

For example, in April 2024, an FDA inspection at Sheng Kee Bakery found employees handling food after touching cell phones, while key machinery was left uncleaned between shifts. These violations weren’t just minor infractions—they meant products were exposed to high contamination risks before reaching consumers.

The Regulatory Crackdown: Why Are Authorities Stepping In Now?

Food regulators are not new to the risks of bakery contamination, but recent events have forced them to take a more aggressive stance.

Take the case of Mena Food Group, LLC, which in August 2024 was issued an FDA warning letter for failing to control environmental pathogens in its ready-to-eat bakery facility. The FDA found that:

• There were no preventive controls in place to stop contamination.
• Allergen labeling violations increased risks for sensitive consumers.
• Facility conditions were poor, with unclean surfaces and storage issues.

Similarly, in October 2024, Haldiram Snacks Pvt. Ltd. (India) was placed under Import Alert 99-43, effectively banning its bakery products from entering the US due to unsanitary manufacturing conditions.

These actions signal a major shift in regulatory enforcement. Where bakery products once escaped intense scrutiny, agencies are now treating them as high-risk—particularly for facilities that fail to implement preventive controls.

How Can the Industry Fix This Problem?

The rise of Salmonella in baked goods is not a mystery, nor is it unsolvable. However, fixing the issue requires a complete mindset shift—from assuming that “baking eliminates all risk” to recognizing that contamination can occur at multiple points in production.

Key Steps Bakeries Must Take:

1. Heat-Treating Flour

   • Major brands are now offering heat-treated flour to eliminate bacteria before use.
   • Companies should prioritize suppliers that implement these safety measures.

2. Strict Temperature Control for Dairy-Based Fillings

   • Pasteurization should be mandatory for all egg- and dairy-based components.
   • Storage conditions must be rigorously maintained, particularly for refrigerated products.

3. Stronger Post-Baking Hygiene Measures

   • Regular sanitation of equipment, cooling racks, and slicing machines is critical.
   • Employees must be trained in strict hygiene practices to prevent cross-contamination.

4. Routine Microbial Testing

   • Final products must be tested for bacterial presence before distribution.
   • Random sampling of raw ingredients can help identify contamination before it spreads.

Can Regulation Solve This Alone?

While stronger enforcement from regulators is necessary, real change has to come from the industry itself. Preventive measures are not just about compliance—they are about protecting consumer health.

If manufacturers fail to act, we will likely see even stricter regulations in the coming years, possibly including:

• Mandatory flour pasteurization for all bakery products.
• Stronger import restrictions on high-risk bakery goods.
• Expanded environmental monitoring requirements for bakery facilities.

The choice is clear: proactive safety reforms today or heavier regulation tomorrow.

Conclusion

The surge in Salmonella cases in bakery products is not just a random occurrence—it is a direct result of overlooked contamination risks, poor hygiene, and regulatory gaps.

For too long, the industry has relied on the assumption that baking is enough to kill all bacteria. The reality, however, is that raw ingredients, post-baking handling, and unsanitary facilities create multiple points of vulnerability.

The recent FDA and international regulatory actions signal that change is coming—whether manufacturers are ready or not. The companies that take action now—by implementing stricter controls, supplier verification, and proactive safety measures—will be the ones that stay ahead of the curve.

Those that don’t? They may soon find themselves under government scrutiny, product recalls, or even legal action.

The future of food safety in the bakery industry depends on how the industry responds today. The real question is: Will it act before the next outbreak forces its hand?