My Healthy Protein Muffins

My wife has a need for a good, quick, high protein & high fiber breakfast. She is in medical school and has to get up really early most days to go to the hospital and so she doesn’t have time anymore to eat her normal breakfast of either oatmeal or Egg Beaters. Her default option is a so called “power” or “protein” bar of any of a variety of brands. The problem is most of those bars contain lots of extra simple sugars and other sweeteners, and they also contain a lot of preservatives and other junk. When you eat simple sugars your body ends up burning them really quickly and then has to use insulin to counteract them, this results in cyclical manic & depressive metabolism in your body and it isn’t healthy, and it just makes you want to eat more. The more complex your food is, such as complex carbohydrates & protein, the longer it takes to digest and the more even your metabolism will be. This will help keep you energized longer and feel fuller.

So I decided I could figure out for her a muffin recipe that’d give her everything she wanted, and still taste good. These muffins are extremely nutritious and taste like carrot cake. Here is the recipe:

Flax Carrot Cake Protein Muffins

Healthy Protein Muffins

  • 1 Cup Stone Ground Whole Wheat Flour
  • 1/2 Cup Soy Flour
  • 1.5 Cups Flax Seed Meal
  • 1 Cup Soy Protein Powder
  • 3/4 Cup Rolled Oats (Oatmeal)
  • 1/3 Cup Chopped Walnuts
  • 1/2 Cup Splenda Brown Sugar Blend
  • 1/2 Cup Normal Splenda
  • 2 Cups Skim Milk
  • 3 Medium Granny Smith (green) Apples, Pealed
  • 1 Cup Shredded Carrots
  • 1/2 Cup Egg Beaters or Egg Whites
  • 1 Cup Raisins
  • 1 tsp vanilla extract
  • 1.5 tsp ground cloves
  • 1.5 tsp nutmeg
  • 1.5 tsp ground ginger
  • 2 tbsp cinnamon
  • 1 tsp salt
  • 1 tbsp olive oil
  • 4 tsp baking soda
  • 2 tsp baking powder
  • (optional) 1/4 cup pomegranate or other high antioxidant fruit juice (the expensive stuff in the small bottles).
  1. Preheat oven to 350 degrees. Grease muffin pan (spray with non-stick spray) or line with paper liners.
  2. In large bowl mix together wheat flour, soy flour, soy protein powder, splenda, splenda brown sugar blend, salt, flax seed meal, oatmeal, cinnamon, cloves, nutmeg, ginger, baking soda, baking powder.
  3. In food processor process carrots until you have 1 cup, usually 2 cups or more whole carrots goes into making 1 cup of finely shredded carrots. Set aside.
  4. Peel, core and quarter your apples. Process in food processor until finely & evenly shredded.
  5. In large bowl mix together shredded carrots, shredded apples, raisin, and walnuts until it comes to an even consistency.
  6. In large bowl combine 2 cups of milk, egg beaters, vanilla extract, and oil (and optional fruit juice). Whisk rapidly until it gets foamy, about 5 minutes.
  7. Pour milk & egg mixture into flour mixture and fold together using a large spoon or spatula, do not over mix and stop once you no longer see any dry ingredients.
  8. Fold apple & carrot mixture into milk & flour mixture using a large spoon or spatula, stop when all ingredients seem evenly dispersed.
  9. Ladle mixture into muffin pan, filling each cup to the very top, even overfilling slightly. Due to the protein there shouldn’t be too much rise. Should make about 18 muffins.
  10. Bake in 350 degree over for 25 minutes or until toothpick inserted in center comes out clean.

So, that is the recipe, now lets talk about it.

First I want to cover the ingredients. Stone ground whole wheat flour is the best kind of wheat flour you can buy, the stones give it a coarser grind and so more of the wheat kernels get into the final product, this increases the protein & the fiber. Mixing in soy flour gives added soy nutrition, more protein, and more fiber, including soluble fiber (stuff really good at cleaning out cholesterol). Flax seed is one of the healthiest foods to eat on the planet, it contains more omega-3 fatty acids than any other plant source (that I know of anyways) it contains large amounts of protein, and large amounts of fiber, without as much fat as other nuts. The buns I buy have flax in them, the pasta I buy has flax in it, and I add it to things I bake (even cookies and meatloaf). Then let us consider the soy protein powder. This is just pure protein as derived from soy, it includes soy antioxidants and is of course a great source of lean protein. Finally among the dry stuff we’ve got the oatmeal, which adds fiber, soluble fiber, and even some protein.

The wheat flour is available at most stores, my local stores also carry the soy protein powder, the flax seed meal, and the soy flour. They don’t carry it in large quantities so you might have to look harder, but they do carry it. Try looking down the baking isle by the speciality flours or gluten free fair, or if there is a healthy living or organic food section in one of the dry goods isles. If you cannot find it at a store you can buy it online at say Amazon or find it at a health food or nutrition store.

Moving on, the muffins also contain a lot of carrots & apples. This ups the fiber and provides vitamins, minerals, and antioxidants. It makes the muffins a serving of fruit & vegetables for your daily needs. Eating healthy isn’t just about eatting fewer calories, but also about eating more nutritious foods, apples & carrots are both highly nutritious.

We’re using 2 cups of skim milk in the muffins, this is a lot of liquid but all the protein based dry ingredients really need liquid to balance them out. The milk provides good milk protein, which is just about the highest quality protein you can get outside of meat, calcium of course, as well as typical vitamin D.

The muffins use Egg Beaters or egg whites instead of normal eggs. Egg Beaters are just egg whites that have had food coloring added (to look yellow) and some vitamins added. By not including any of the yolk you cut down on around 70% of the calories and 100% of the cholesterol in eggs. Normally this might result in a less moist baked product, but all the fruit in these muffins contribute adequate moisture.

We also add 1 tbsp of olive oil to counteract some of the stickiness of the protein and provide help with residual moisture. You could use any oil, but olive oil is healthier and provides more vitamins and antioxidants.

We’re only using a 1/3 of a cup of chopped walnuts, other recipes might call for more. The issue with walnuts is they’re basically a less healthy version of flax seeds. They contain less fiber, less protein, and less omega 3 fatty acids, but many more calories. Compared to any other nut walnuts will be healthier, but compared to flax seed meal they’re just not. So we’re only adding the walnuts for crunch factor, but still they do contribute protein, fiber, and omega 3s, just not as much as the flax does.

The raisins contain a lot of sugar, but it is all natural unrefined sugar, so that isn’t so bad. Raisins also contain tons of antioxidants, they’re one of the most antioxidant rich foods, and they’re still a little juicy so they provide a nice texture contrast with the nuts when eating the muffins.

Then there is the Splenda. Splenda is a great sweetener that tastes like sugar so you hardly notice the difference. In only a few applications can you not replace sugar with Splenda. In this case we’re using Splenda Brown Sugar Blend & normal Splenda. The Brown Sugar Blend is a blend with real brown sugar, so there are calories there, however it is necessary because brown sugar contains properties that sugar substitutes just don’t. In total using Splenda probably saves 50-100 calories per muffin.

Rounding up the rest of the ingredients are the baking soda & baking powder. These items are what create the bubbles in the muffins that allow them to rise and be fluffy. It is important they not be too old so check the expiration dates on yours, also, if you bake regularly, you may think I’m asking for a lot of both, and I am. This is because all the protein in the mixture requires extra help in rising. Then of course there are the spices, you can add more or less depending on how much you like the carrot cake flavor.

The last ingredient is the optional fruit juice, and really this is optional. If you want a little extra flavor and or antioxidants you can use it. Use the good juice though, the 100% fruit juice of pomegranate, blueberry, mangosteen, acai, or other high antioxidant fruit juice. This juice is usually not stored by the other juice, but usually in a refridgerated section and usually is fairly expensive and comes in smaller glass or plastic containers. I like using it as an additive and I never drink it straight.

So, that is all the ingredients and why I use them.

As far as the cooking method goes, it is very important to mix all the things separately as I have indicated. Firstly you want to mix the dry stuff thoroughly before it gets wet to make sure the baking soda & baking powder as well as the spices get evenly distributed. You cannot overmix it at this stage.

Then you whisk the milk & egg mixture to make sure it gets thoroughly combined but also to create those bubbles that will also help to create air pockets & rise in the final mixture.

Finally you mix the apples & carrots thoroughly to make sure they end up evenly distributed and so the end muffins aren’t like all carrot or all apple depending on which muffin you bite into.

The reason you cannot simply add everything together and then mix is that excessive mixing of the flour once the liquid has been added will cause the protein called gluten to get even more rigid making the muffins even more chewy than they’re already going to be. So you mix the 3 main component mixtures thoroughly prior to mixing it all together so that when it all does come together you have to do as little mixing as possible. This concept is important for just about any baked good, you almost always want to mix the wet stuff & the dry stuff separately before adding them together.

If you end up with 18 muffins and use everything I have mentioned you’ll get the following numbers per muffin:

  • 205.5 Calories
  • 11.08g Protein
  • 5.7g Fiber

Try finding a health bar that contains so few calories, so much protein, and without any added weird or unhealthy junk such as high fructose corn syrup, or any sort of hydrolyzed protein. Also, my muffins contain no saturated fat, no trans fat, and no cholesterol.

So, if you’re trying to lose weight or just want a quick & healthy breakfast, make up a batch of these, and refridgerate them for storage, or freeze them. (All the unsatured fats & proteins in the muffins really can end up going bad quickly, so keep them in the fridge). If frozen you can thaw them as needed by taking one out the night before and putting it on the counter in a container of some sort.

Eat one or two for breakfast, depending on your weight loss goals or calorie needs. If you plan on eating two though don’t eat them at the same time. Eat one, and wait until you’re hungry again (even if it is just 30 minutes) before eating the second one. This will keep your metabolism going and keep your fuller longer.

If you like this recipe, check out my similar healthy chocolate brownie recipe too.


  1. Hey! I just stumbled across your blog this evening and I have to say I am glad I did. I’ve read your articles here and I really like your approach to cooking! I’m looking forward to reading your future articles. Your fellow man cook, JON.

  2. I just found your blog while looking to make healthy muffins for my family, since school’s going to be starting and I will be working soon.
    So thank you very much for shareing this helpfull information!!

  3. I was looking for exactly this type of recipe. Can’t wait to try them!

    Thanks so much for sharing with us! :o)

  4. Thank you! I was looking for the perfect breakfast muffin…might try agave as a sweetener. I don’t like the super-processed aspect of splenda.

  5. There is a conspiracy website out there for pretty much every substance known to man. Don’t buy into the propoganda.

  6. Thanks so much for this recipe. I’ve been trying for awhile to make a good protein healthy muffin, and this recipe is fabulous! I made some changes, such as using spelt for half the flax meal (because I don’t love the flavor of that)and increased the fat just a tad (total 1/4 cup canola oil) but left out the walnuts. Also used brown sugar, just 1/2 cup instead of the splenda, because I don’t like using sweeteners.

    I think next time I will jsut folow your recipe exactly and see how I like it. I’m just a bit nervous about all that flax meal.

  7. Any idea what the fat content per muffin is? I love them…and my kids like them too! Thank you so much for creating and sharing this recipe!

  8. Refrigerating or freezing the muffins…is this the finished product or the mixed ingredients before baking? Thanks! Great recipe!!

  9. finished muffins

  10. Hey Chris, can I substitute whey protein powder for the soy protein powder? Also, do you have the other numbers per muffin, such as fat and total carbs? I love your blog, as I am avid at trying to eat healthy to have a long, healthy life!

  11. Whey I do not think cooks as well as soy, if whey is all you can find (or if you’re allergic to soy) I guess you could try it, but in my experience whey does not play well in baked goods.

    In contrast, soy is gross in smoothies. So I use whey for smoothies and soy for baking.

    I don’t have total fat, there is 0 saturated fat so all the fat is the hearth healthy kind, nor did I pull out total carbs. But if you were thinking net carbs, with there being so much fiber, it’d have to be near 0.

  12. Heather says:

    When I finally got these in the oven, I was certain they would be rocks…or some other kind of inedible mass.

    Wrong! THey are wonderful. Moist, just barely sweet–mostly the apples and raisins. Fill me up. SOOOO good.

    I used regular brown sugar, but a little less. And honey for the regular splenda. And I included the POM juice. I also got 24 muffins, but I admit…I didn’t measure fruit and stuff–I just eyeballed.

    Next time…just for kicks, I’m including a handful of butterscotch chips…I can’t be totally healthy.

  13. Gabrielle says:

    I stumbled onto your site while surfing for a high protein muffin recipe and boy, am I glad I did! I’m going to make these muffins today.

    I buy my flax seeds in bulk and grind them myself instead of buying flax seed meal. I hope there won’t be a difference in the finished product.

  14. Kelley says:

    I too have been trying to find a protien rich muffin recipe.

    Yours looks incredible and I cannot wait to try it.

    I have been on “The Zone” and the recepie’s are limited as the book is over ten years old.

    Thanks so much :-)

  15. Use maple syrup, honey, molasses…anything but splenda!!!

  16. These are DELICIOUS! Moist and flavorful, great texture, not dense or hard or dry at all as I might have expected from the protein powder and flax meal. Nice work and thanks for sharing!

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