Baking with Protein Powder

Does Baking Whey Protein Denature it?  AGN Roots Grass-Fed Whey Protein

Cooking Whey Protein Powder

Cooking with whey protein is a great idea, and at AGN Roots, we highly encourage it. In this article, we provide the details on several topics commonly searched for on our site, these include -

  • Can you cook protein powder?
  • What Impact will whey (WPI vs. WPC) have on my cookies or cakes?
  • Can I cook whey protein powder without destroying it?
  • Will baking with whey protein powder denature the protein?
  • Is Denatured Protein still bio-available?

Can You Cook Protein Powder?

As the world continues to make advancements in health and wellness, the baked goods industry is not sitting idle. When we think of novelties like cakes and cookies, our minds naturally wander to a negative outcome that often includes gaining weight or becoming unhealthy.

Counter to many beliefs, adding something healthy to a cookie does not make the cookie any healthier. Adding protein to anything these days, especially for those chasing daily macro targets, will reduce the burden on the mind acquired through the consumption of the cookie alone.

The addition of whey protein to a cookie that otherwise would taste and look the same is a net benefit to the consumer with one reasonably large assumption; the consumer would be eating the cookie with or without the protein added.

Making protein cookies at home is a beautiful idea as you control all the ingredients and focus on quality. In stark contrast is the idea of buying a pre-wrapped cookie that's labeled "protein cookie" at the grocery store.

The protein bar and cookie market are essentially the same as the cookie and cake market. Most protein cookies include the following ingredients that do nothing in terms of getting you closer to your best version -

  • Butter (Cream) & Cocoa Butter
  • Oligo-fructose or Super Sweetener (Stevia / Erythritol)
  • Calcium Caseinate & Sodium Caseinate
  • Natural Flavors
  • Xanthan Gum

If you are considering protein cookies - The healthiest protein cookies are always made at home.

If you have a great recipe you would like to fortify with whey protein powder; the following sections will explain what you can expect in terms of how adding whey protein to your favorite baking recipes will impact the final product.

    Baking with Whey Protein Concentrate (WPC)

    The higher the amounts of whey protein added to the dough, will lower the post-baked density. The reduction in density speaks to the final product producing a fluffier (air-filled) yield. Applying this to your baked goods, the cake or cookie you add whey protein concentrate to will take more volume and rise to levels 18% more than usual [1].

    Adding a whey protein that contains 20% fat and sugar to a homogenous rising dough will create the same effect as adding eggs to a brownie batter.

    The explanation of the increase in air incorporation is due to the protein denaturation paired with gelatin functionality associated with the phospholipids (fats) contained in WPC. The same also goes for many whey protein tubs with Xanthan gum designed to create a thick smoothie texture.

    As the heat denatures the 3rd and 4th structures of the protein, the native bends and folds unravel as protein aggregation occurs. The resulting structure is not organized and resembles a rat's nest cluster.

    The protein clusters pitch larger surface areas of aeration (capture more air) during the cake rise. Like a hot air balloon, the gelation functionality, gums, or the fats in WPC will trap the air pockets and make it difficult for them to escape.

    Learn More: What Are Protein Structures - (Image)

    Baking with Whey Protein Isolate (WPI)

    When adding AGN Roots to a dough, expect the impact on the density of the baked good to remain unchanged. Cakes, cookies, or pizza doughs fortified with Whey Protein Isolate (WPI) will yield significantly lower volumes than if a WPC with a Xanthan gum component is part of the mix.

    Due to the lack of gelation functionality in WPI, no gels contain the rising gases (air bubbles). As the dough begins to rise due to heat, the non-gelled protein cluster structure allows the air to escape, reducing the sponge effect (porosity).

    Does Heat Denature Whey Protein?

    Yes, heating or cooking protein powder will most likely solicit protein denaturation followed by protein aggregation. Denaturation to a finite degree is typical and occurs naturally with little impact on bio-availability or the nutritional value of the whey. However, severity matters and as denaturation progresses the value of the protein to your body decreases.

    Does Heat Destroy Whey Protein?

    Heat introduces kinetic energy, which excites the polypeptides via thermal motion. At a point, the thermal movement ruptures the weakest intermolecular forces. The impacted parties include nonpolar and electrostatic interactions paired with the physical disulfide bonds, all of which work in harmony to hold the protein in its native conformation [7].

    When the temperature increases to the degree that it's wholly unfolded (secondary & tertiary structures overcome), the protein gains the potential to aggregate.

    Aggregation is the scrambling of disulfide bonds, the modification to side-chains, and other polypeptides' formation cross-links.

    Aggregation begins when the nonpolar interaction between proteins (denatured via thermal exposure) whose hydrophobic groups reorient outward towards surrounding water and thus adopt a reduced energy state.  

    Learn More: What is Denaturation?

    Does Heat Permanently Denature Whey Protein?

    Yes and No. The answer depends on the severity of the heat and the exposure circumstances. The integrity of each protein structure is dependent on different types of bonds. Furthermore, there is a difference between denaturation to the degree of nutritional loss and reversible changes to the shape with no damage to individual amino acids. Let us look at the dependencies closer.

    The initial stages of deformation of the protein structures occur when the 3rd or 4th protein structure begins to unravel. Much of this particular unraveling is reversible and, in this case, referred to as "temporary denaturation." When heat is applied, the protein will change shape, and when the heating exposure is no longer present, the protein returns to its native state.

    When the 3rd and 4th structures face exposure from denaturing forces, there is zero impact on nutrients or bioavailability. The protein is said to be "unfolding" or "unraveling".

    3rd Protein Structure (Tertiary)

    • Salt Bridges & Ionic interaction
    • Disulfide bridges
    • Hydrophobic interactions & London dispersion forces
    • Hydrogen Bonding

    4th Protein Structure (Quaternary)

    • Aggregation of two or more polypeptide chains into a single functional unit

    When denaturation begins to alter the 1st and 2nd structures of the protein, the protein powder is losing its value. The individual amino acids and their intermolecular integrity are essential for your body to receive intact.

    When the body ingests severely denatured whey protein (low quality), it's not the end of the world. However, the ability to get the most out of the whey now depends on your body's ability to pick up the slack and sift through the good and bad components to get what it needs.

    1st Protein Structure

    • Individual amino acids
    • Bound by Peptide bonds

    2nd Protein Structure

    • 𝛂 Helix & 𝛃 Pleated Sheets
    • Bound by Hydrogen bonds

    Does "Denaturation" Destroy The Benefits of Whey Protein?

    The answer to this question depends on a few factors including:

    • Severity of the denaturation
    • Mechanisms of denaturation
    • Protein Macro vs Proteins Fractions

    Our intestines absorb individual amino acids cleaved and delivered by enzymes [8]. These protein pieces are fully bioavailable and utilized in the form of single amino acids or various peptide forms that include

    • Dipeptides
    • Tripeptides
    • Oligopeptides

    Where digestion and bio-availability become crippled is when our digestive enzymes have issues recognizing the modified structures. At AGN Roots, we preach just as much about digestive health as we do quality food and whey; one does nothing without the other.

    Some stomachs can put Humpty Dumpty back together again no matter how shattered; others fail to get past a minor crack in the shell. 

    At What Temperature is Whey Initially Impacted by Heat?

    Whey proteins, in general, are sensitive to heat at temperatures above 70°C (158°F). When exposed to temperatures beyond this, denaturation is natural and inevitable.

    When cooking with whey protein powder, two main factors that contribute to the denaturation of the protein structures include temperature and pH.

    When does Denaturation Cause Bio-Availability Loss?

    Maximum denaturation to the point of individual amino acid deformation (nutritional value losses) occurs in two scenarios -

    1. At the extremes of the pH or temperature spectrums independent of each other
    2. When exposure includes both pH and temperature stresses simultaneously, neither at the end of the spectrum

    The scenarios above highlight the importance of controlling temperature and pH where possible as denaturation is not linear. When these forces are applied simultaneously, and outside a neutral range, considerable complexity introduces the potential for stochastic impacts.

    If cooking something very acidic and at sustained temperatures above 350F for 30 min, you may not be getting the nutrients you think you are from a delectate grass-fed whey.

    In terms of the protein fractions that drive you to invest in a high-quality grass-fed whey, most of these items are much more fragile than the complete protein macro itself.

    Preservation of the native structures occurs between pH 6-7 and moderate baking temperatures at 350°F for less than 30 min, assumes a steep temperature gradient or homogenous temperature [3].

    Is Whey Protein Powder Fragile? 

    The web is chock-full of wrong information on this topic. Most of the talking points are either anecdotal or extrapolated from scientific studies focusing on eggs or milk.

    In a perfect world, YouTube "fitness" personalities should have to cite their wisdom origins like any other credible publication. Whey isolate is not whole food like eggs or milk. Although this sounds ridiculous to spell out, eggs and milk are wildly different from isolated, dehydrated, whey protein powder.

    Both eggs and milk have properties that add layers of stability and protection to the more fragile whey protein fractions. Whey protein in isolated powdered form is not as near resilient to thermal exposure compared to proteins within their whole food.

    Furthermore, most online forums or blogs, when parting information on the topic of denaturation, are referring to the Protein macro itself and make no references to the fragile protein factions at risk in a high-end genuinely grass-fed whey protein isolate.

    Learn More: Whey Protein Factions Explained

    In many cases, the basis of design for powdered milk products like protein powder or baby formula is stability first, with nutrient sustainability taking a backseat.

    A common and logical thought for many is as follows -  

    "if the milk has already undergone pasteurization at high temperatures, then baking with the whey powder is fine." 

    Where this logic falls short is twofold -

    1. During sterilization and pasteurization, the casein micelles and other solids protect the whey and serve as a denaturing buffer against extreme temperatures and pH ranges.
    2. Even high-temp-short-time (HTST) pasteurization  (the most common method globally) is limited to 161°F for 15 seconds. However, in New Zealand, where standard practice for dairy set for export is ultra-high temperature pasteurization (driven by stability purposes to survive shipping), this thought becomes valid. Flash heating anything to 400°F is damaging. 
    Click Here for a High-Resolution Pasteurization Chart

      When you add a whey isolate powder to an item you plan to put in the oven, the whey is exposed and unprotected which is why denaturing can be an issue in many recipes, especially when the item is also acidic or basic.

      Doesn’t My Stomach Acid Denature the Protein?

      Yes. As a statement of fact, the stomach provides the environment which allows the deconstruction of proteins down to usable amino acids. By definition, these proteins undergo denaturation via enzymes – but not destroyed by acid.

      Our stomachs don't destroy the nutrient content of whey powder because proteins (amino acids) are very resilient to single extreme-factor conditions.

      Our stomach operates routinely with pH values ranging from 3.0 – 6.0; this is acidic. In terms of temperature, however – 98.6F is a very comfortable and stable temperature for proteins.

      The denaturation from low pH doesn't extend to the intermolecular integrity of each amino acid. The purpose of the low pH is limited to creating the perfect environment for enzymes to cleave the peptide bonds in the 1st structure effectively. The pH value serves as the single extreme factor, whereas the other denaturing forces are essentially negligible.

      Learn More: What Enzymes Break Down Protein?

      Bioactive Non-denatured Grass-fed Whey Protein

      What protein fractions are at risk?


      Lactoferrin begins to degrade when the following conditions exist visibly;

      • pH between 2.0 and 3.0
      • Temperatures are between 100°C - 120°C (212°F-248°F)
      • Time at exposure 5 min

      For Lactoferrin, although denaturation will occur, the benefits around antibacterial activity and iron-binding behaviors remain intact [4].

      Bovine Serum Albumin (BSA)

      BSA is highly sensitive to temperature and pH changes, more so than lactoferrin. At temperatures > 70°C (158°F) for more than just a few minutes, irreversible protein aggregation occurs with BSA [5].

      BSA is germane to authentic grass-fed dairy and not in factory-farmed protein powders; thus, 99.9% of consumers are affected. The key here is to not cook with grass-fed whey if you are looking to reap benefits associated with BSA benefits.


      Beta-Lactoglobulin contains a lot of the muscle-building elements that whey protein enthusiasts love. These include branched-chain amino acids (BCAAs). Beta-Lactoglobulin is relatively robust and is thermally stable as Ph values around 3.0. Where this protein fraction begins to fail is described in the following environment. 

      • pH > 9.0 (unfolding of the coils)
      • Temperatures > 80C (176F) losses in the secondary structures [6]
      • Time at exposure 10 hours beta-lactoglobulin becomes noticeably denatured.

        How to Cook with Whey?

        Below are three tips to protect your grass-fed whey nutrients while baking or cooking. The tips below serve a specific intent of either reducing the severity of denaturation by either limiting time exposure or shielding the whey with other natural protective ingredients.

        1.) Utilize Natural Protectorates (milk, eggs, butter)

        Pre-mix the whey powder with either a common baking ingredient that will naturally provide thermal protection. 

        • Whole Milk - A suit of casein armor
        • Eggs - Gelatinous egg whites for protective services
        • Melted Butter - Utilizing fat + Make it taste great

          2.) What Pan is Best to Bake Whey Protein Cookies? 

          The goal is to utilize a material that evenly distributes heat and doesn't absorb it; instead reflects. From a material selection point of view, consider using silicon or anodized aluminum.

          When possible, utilize silicon or another insulating material (low conductivity). Anodized aluminum pans reflect heat and don't absorb it; this allows a temperature reduction when you turn off the oven or remove the baked good from the heat.

          Standard aluminum will heat up quickly, and denaturation gradients will propagate like a tough corner piece brownie (more heat exposure versus the soft middle). 

          The following materials will absorb heat and keep your baked goods exposed to the thermal elements much longer than needed. 

          • Glass
          • Stone
          • Clay

          You can adjust cooking time to account for cool-down exposure or remove the baked good immediately from the cooking pan after removing it from the oven.

          3.) When to Avoid Adding Whey Protein to a Recipe?

          If the recipe calls for acids, consider drinking a whey smoothie when enjoying your cookie. Chocolate chips are "ok"; they are acidic; however, the acidity with the chip will not impact the whey. Acidic ingredients to avoid include -

          • Citrus juices
          • Vinegar
          • Chocolate sauces
          • Apple sauce
          • Baking powder

            Learn More: AGN Roots Grass-Fed Whey Recipes Page  

            [1] Camargo, Liziane, et al. “Effect of Whey Protein Addition on the Nutritional, Technological and Sensory Quality of Banana Cake.” International Journal of Food Science & Technology, 22 June 2018,
            [2] Efigênia, Maria, et al. “Effect of Heat Treatment on the Nutritional Quality of Milk Proteins.” Science Direct, International Dairy Journal, 1997, 
            [3] M.A. Nielsen, S.T. Coulter, C.V. Morr, J.R. Rosenau, "Four Factor Response Surface Experimental Design for Evaluating the Role of Processing Variables Upon Protein Denaturation in Heated Whey." Journal of Dairy Science, Volume 56, Issue 1, 1973,
            [4] Hiroaki Abe, Hitoshi Saito, Hiroshi Miyakawa, Yoshitaka Tamura, Seiichi Shimamura, Eiji Nagao, Mamoru Tomita, "Heat Stability of Bovine Lactoferrin at Acidic pH." Journal of Dairy Science, Volume 74, Issue 1, 1991,
            [5] Borzova, Vera A et al. “Kinetics of Thermal Denaturation and Aggregation of Bovine Serum Albumin.” PloS one vol. 11,4 e0153495. 21 Apr. 2016, doi:10.1371/journal.pone.0153495
            [6] Boye, J I et al. “Effects of physicochemical factors on the secondary structure of beta-lactoglobulin.” The Journal of dairy research vol. 63,1 (1996): 97-109. doi:10.1017/s0022029900031575
            [7] Davis, P J, and S C Williams. “Protein modification by thermal processing.” Allergy vol. 53,46 Suppl (1998): 102-5. doi:10.1111/j.1398-9995.1998.tb04975.x
            [8] Yu, Tzer-Yang, et al. “Cooking‐Induced Protein Modifications in Meat.” Wiley Online Library, John Wiley & Sons, Ltd, 24 Nov. 2016,
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