Hot Takes on Baked Goods

More than 2,000 baked foods are produced in the United States, with thousands more worldwide. As such, the American baking industry is a massive component of the food sector, generating over $186 billion in total economic output. Baking uses dry heat—usually in an oven, but also in hot ashes or on stones—without direct flame exposure. While bread is the most common product, the baked goods category also includes cakes, pies, cookies, pastries, muffins, and more. Baking enhances flavor, extends shelf life, and serves as a microbial kill step to help ensure food safety.

Here, we explore best practices in baked goods processing, from ingredient selection and dough development to fermentation, baking, and cooling. This article highlights how careful control of each step helps ensure consistent quality, safety, and consumer satisfaction, while also addressing sustainability and efficiency.

Baked Goods Inputs

Next time you walk through your local supermarket, look at the different flours available. There are products made from wheat, rye, barley, corn, peas, and other sources, along with organic and gluten-free options. There are also wheat flours with differing levels of gluten that are labeled for specific applications. For example, pizza doughs and strudel use high-gluten flour because these products require high dough strength. Wheat flours contain between 8% and 15% gluten, with winter wheat varieties typically having higher levels.

Self-rising flours are also available and contain leavening agents such as baking powder and other materials that release carbon dioxide and contribute to dough rise during baking. Depending on the product, bakers may choose either fast- or slow-acting baking powders. Slow-acting products release gas during baking once the flour and other ingredients begin to gelatinize, trapping the gas and yielding the proper volume and structure.

Flour and eggs serve as structure builders during baking, whereas fat in the form of shortening serves as a tenderizer. When shortening is beaten, it entraps air prior to the incorporation of other ingredients. During baking, the shortening melts and releases the entrapped air, contributing to leavening and final structure. These characteristics are influenced by the plasticity of the shortening and the use of emulsifiers such as soy lecithin. Emulsifiers are compounds that lower the surface energy between two immiscible liquid phases—oil and water—thus facilitating the dispersion of one phase into the other. Hard fats and emulsifiers yield products such as flaky croissants.

Industrial baking demands scientific knowledge of both processing and ingredient functionality.  

Many other ingredients are used in baking, especially in bread. These include vitamins, fiber, iron, and mold inhibitors. Vitamins commonly found in enriched flour include thiamine, niacin, and folic acid. Mold inhibitors include calcium or sodium propionate, sorbates, benzoates, parabens, and acetic acid. These ingredients extend shelf life and reduce food waste. Who has not thrown away bread that was beginning to turn green or blue? Clean label alternatives include raisin juice, whey, and vinegar.

Every ingredient has a function, and they all come together during baking, which accomplishes several processes, including gas evolution and expansion; coagulation of gluten and eggs; gelatinization of starch; and dehydration through water evaporation. Other essential functions are flavor development; color changes due to Maillard browning and other chemical reactions; crust formation and darkening due to Maillard browning and sugar caramelization; and microbial inactivation.

Microbial Food Safety

For many years, the baking process was assumed to ensure food safety without formal validation. With the implementation of the U.S. Food and Drug Administration’s (FDA) Food Safety Modernization Act (FSMA), baked goods manufacturers began reassessing their processes to verify effectiveness. Even before FSMA was finalized, many companies, working with academia and industry associations, conducted validation studies across a range of baked products.

Early research found that while plain products heated uniformly, items with inclusions such as nuts, seeds, chocolate chips, or fruit pieces did not. Dense inclusions heated more slowly, leading to new requirements for ingredient suppliers to provide documentation confirming that their products are pathogen-free.

Validation is now mandatory for all food processors under FDA jurisdiction and must be repeated every three years or when significant process changes occur. Salmonella remains the primary pathogen of concern for baked goods due to its heat resistance in low-moisture, high-fat environments. Ingredients linked to outbreaks include flour, eggs, dairy, chocolate, nuts, and spices. Many bakers now use heat-treated flour. In fact, some flours on the market include the statement, “Say no to raw dough. Flour is a raw ingredient. Bake fully before enjoying.”

Bakers must comply with FDA’s Hazard Analysis and Risk-Based Preventive Controls for Human Food (HARPC) requirements, which mandate identification of potential biological, chemical, and process-related hazards and implementation of controls to address them (FDA 2018). To support compliance, the American Institute of Baking (AIB) maintains a database of validation studies for products such as breads, muffins, cookies, tortillas, and doughnuts. AIB also offers a free Baking Process Kill Step Calculator that allows bakers to input time and temperature data to calculate process lethality for Salmonella destruction and generate documentation for FSMA validation (AIB 2015).

Chemistry Issues and Concerns

Several chemical food safety concerns must be addressed in baked foods, as outlined by FDA in Appendix 1 of its HARPC draft guidance (FDA 2018). These include natural toxins, mycotoxins, and undeclared colors or additives. The first two concerns are generally addressed through a company’s vendor quality program.

Aflatoxins produced by Aspergillus flavus have been associated with grains, nuts, and cereals commonly used in baking. Fumonisins are produced by Fusarium species and are associated with corn and cornmeal. Regulatory agencies have established limits for these compounds.

Undeclared colors or additives are typically controlled through batching procedures within the processing facility. Allergens pose the greatest chemical hazard. Of the Big Nine allergens, seven—wheat, soy, egg, dairy, peanuts, tree nuts, and sesame—are commonly used in baked goods. Bakers must prevent cross-contact and ensure accurate labeling. Many bakery recalls listed on the FDA website involve allergen mislabeling. Best practices for allergen and additive control include the following:

• Conducting pre-operational checks to verify that batching lines and vessels are clean
• Confirming that correct ingredients and allergens are properly managed and documented
• Maintaining sanitary facility design, including ventilation above batching areas to reduce dust from flours, grains, seeds, and nuts

Water Impacts

Water is a key ingredient in many baked foods, especially breads, rolls, and other products made with fermented dough. Bakers must understand the chemistry of the water used in their operations and may need to treat it to optimize performance and product quality. The chemistry of water can directly affect dough behavior. Two critical parameters are pH and hardness, which is measured as calcium carbonate concentration in parts per million.

Water makes up approximately 40% of total dough mass. Elevated mineral levels can adversely affect dough and final bread quality. Water with moderate hardness, typically in the 50–100 ppm range, is considered ideal for baking because minerals at these levels strengthen dough structure. Hard water, defined as greater than 120 ppm calcium carbonate, can overly strengthen gluten and negatively affect fermentation by inhibiting water absorption by bread proteins.

The chemistry of water can directly affect dough behavior.  

If water is too hard and not softened, operators can compensate by adding more yeast, reducing yeast food and other mineral-containing ingredients, or adding acids such as yogurt.

Soft water can also create problems because low mineral levels lead to weak gluten structure, producing soft and sticky dough. Although soft water may produce bread with good volume, texture and color may be negatively affected. These issues can be addressed by using yeast or adding dough salt to the dough.

Water pH must also be monitored. High-pH water can raise dough pH above the optimal fermentation range of 4 to 5. Bakers can adjust alkaline water by adding acids such as acetic acid, lactic acid, or monocalcium phosphate, an ingredient commonly found in baking powder.

From Dough to Delight

In today’s baking industry, ensuring food safety and consistent quality requires a deep understanding of both science and process control. While baking at home is often an art, industrial baking demands scientific knowledge of both processing and ingredient functionality. Validating microbial kill steps and managing allergens are essential and ongoing responsibilities to ensure safe, wholesome baked goods.

Following FSMA guidelines, implementing supplier verification programs, and leveraging tools such as AIB’s Kill Step Calculator help safeguard products and consumers. Bakers must also understand the impact of seemingly simple ingredients like water, as well as external factors such as altitude. A baker in Denver faces different formulation challenges than one in San Francisco.

As clean label trends, automation, ultra-processed food scrutiny, and sustainability shape the future of food processing, success depends on combining proven best practices with innovation. Doing so ensures that every loaf, cookie, and cake delivers safety, quality, and the unmistakable satisfaction of expertly baked food—and keeps customers coming back again and again.