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Home › Recipes › By Type › Breakfasts
★★★★★49 Comments

Flourless Chocolate Chip Protein Muffins

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by Lindsay Cotter Published: Jun 18, 2022

Dairy-FreeGluten-FreeVegetarian
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muffins in a pan with hands holding edges

Your new favorite breakfast or grab-n-go snack, flourless chocolate chip protein muffins are a healthy recipe you’ll love! Low sugar, high protein, and flourless, they’re light, fluffy, and good for you, too! Make them ahead of time to enjoy all week. Nut free option.

Chocolate chip Muffins in muffin pan. Sitting on cooling wrack. Two muffins out of pan and one with bite taken out. Spoon of sugar above pan

More Than Your Average Muffin

Can anyone say no to a good muffin? From healthy carrot cake muffins, to gluten free apple oatmeal muffins, dark chocolate vegan muffins, and everything in between, there’s a recipe for every taste bud! Honestly, we love ‘em all and have a batch or two on hand at all times. However, some versions like those found in stores can be high in sugar and contain some not-so-great ingredients. They may taste incredible, but they don’t keep you fueled for long! 

chocolate chip protein muffins in muffin pan

So, we decided to give everyone’s favorite chocolate chip muffins an upgrade and turned them into protein muffins instead! They’re every bit as delicious as a standard muffin – just a whole lot more nutritious! Not to mention, they’re gluten free, flourless, and even have a nut free option to meet all your needs! 

Are Protein Muffins Actually Healthy? 

You bet they are! Unlike typical muffins that are made with refined flour and sugars, our protein muffin recipe utilizes whole ingredients that are full of vitamins and nutrients! Then, we added a boost of protein and lowered the carbs just a tad to help stabilize your blood sugar and keep you satisfied for hours.  

ingredients for flourless chocolate chip protein muffins on a baking sheet

Ingredient List

For this protein muffin recipe, we kept standard baking ingredients like salt, vanilla extract, and baking soda but gave everything else a nutrient-rich upgrade! Here’s what you’ll need: 

  • Gluten Free Rolled Oats – Make sure your oats are certified gluten free! When mixed into the batter, they are ground to create a flour-like consistency that provides structure for your muffins and fiber to keep you full!
  • Vegan Protein – Any vegan protein flavor you have on hand works. However, for the best taste and texture, we prefer to use chocolate or vanilla pea protein or a vegan protein blend. Can’t tolerate legumes? We also love using Bob’s Redmill almond protein powder! It also works well for making vegan protein pancakes.  
  • Eggs – Not only are eggs used to help these muffins hold together and become fluffy, but they also boost the protein content even more while also contributing healthy fats! 
  • Non-Dairy Milk – Any non-dairy milk like oat milk, almond milk, coconut milk, or cashew milk can be used for these muffins!
  • Maple Syrup/Honey – Maple syrup (or honey) helps create a sweet taste without the need for refined sugars.
  • Natural Creamy Nut Butter – Nut butter helps elevate the depth of these muffins while contributing healthy fats and a creamier texture. We used peanut butter, but almond or cashew butter could be used as well. Or, for nut free muffins, opt for a seed butter instead!
  • Dairy Free Dark Chocolate Chips (or Sugar Free Chocolate Chips) – All the chocolate flavor with none of the dairy! Dark chocolate is loaded with antioxidants. We’re pretty sure that means you can go back for seconds or thirds! 😉

Allergy-Friendly Alternatives & Flavor Variations

We did our best to keep this protein muffin recipe as simple as possible. However, it can easily be altered to fit your specific needs and taste buds! Take a look at a few of our favorite alternatives and variations below. 

No protein powder? Swap it out for chickpea flour or oat flour and a tablespoon of sugar. (Be sure to take a look at the recipe card below for details.)

Boost the nutrients with fruit! We love to fold in a handful or two of berries to the batter for extra nutrients and fiber. 

Make them extra chocolatey! If you opt for vanilla protein powder but still want that extra chocolate taste, try adding in a scoop of cocoa powder too. 

Spice things up! For a hint of both sweet and savory flavors, add a dash of cinnamon to your muffin batter. 

What Is the Best Protein Powder for Muffin Baking? 

For plant based protein muffins, pea protein yields the best taste and texture. Bonus points if it’s sprouted! Not only is pea protein powder gluten free and vegan, but it also has a mild taste that can easily be incorporated into any baked good.

overhead shot: metal measuring cup inside a bag of protein powder

In addition, it yields the best texture creating light and fluffy muffins instead of dense and grainy ones. 

Pro Tip

Note: If you don’t have pea protein on hand, hemp and rice protein powders yield similar results.

Can I Use Whey Protein Powder?

Yes! If you can tolerate the lactose found in whey proteins, they work just as well for this muffin recipe. Just be sure to adjust the sweetness and baking times as needed. For the best results, we recommend sticking with a whey protein concentrate powder! 

Simple Instructions for the Best Protein Muffin Recipe + Video

These high protein muffins are so delicious and quick to make, you’ll never go back to boxed versions again! Just follow the steps and watch how it’s done below. You’ll have a tasty snack in no time. 

  1. Preheat the oven to 350° Fahrenheit, and add muffin liners to your favorite muffin pan. Or, grease it with a high-quality cooking spray.  
  2. Pulse the oats in a blender until a flour-like consistency is formed. 
  3. Whisk the dry ingredients together in a large mixing bowl until smooth. 
  4. Then, in a separate large bowl, combine the nut butter and maple syrup (or honey) until they are smooth and creamy. 
  5. Next, whisk together the eggs, non-dairy milk, and vanilla in a large measuring cup Working in batches, combine ⅓ of the dry ingredients and the egg/milk mixture into the large bowl of nut butter and maple syrup.
  6. Repeat the process until all of the ingredients have been combined and a cake-like batter is formed. 

    scoop of muffin batter in cookie scooper

  7. To finish, fold in the chocolate chips, and spoon the batter into the muffin pan. 
  8. Bake 18-22 minutes or until the center of your muffins comes out clean with a toothpick. Let them cool completely on a wire rack on the counter before serving. 

Flourless Chocolate Chip Protein Muffins

Stand Mixer Option 

For a more hands-off recipe, we also tested these muffins with a hand mixer! Here’s what to do: 

  1. Beat the nut butter and maple syrup with a paddle attachment. 
  2. Then, at a low speed, slowly add the flour mixture alternately with the egg mixture. Make sure to begin and end with the flour mixture, and mix until the ingredients are just combined. You do not want to overmix your batter! 
  3. Spoon the batter into the prepared muffin pan, and bake at 350° Fahrenheit for 18-22 minutes. Remove them from the oven, and let your muffins cool completely before serving. 

Secret Muffin MakingTips & Tricks

To become a true muffin-making pro, be sure to follow our tried and tested baking tips to ensure your healthy protein muffins are jaw-droppingly delicious every single time. 

Use Oat Flour. To speed up the preparation time, opt for gluten free oat flour instead of whole oats. Just be sure to measure the weight of the flour to match the weight of the oats. (You’ll need around 195 grams.) 

Use Room Temperature Ingredients. When used at room temperature, the eggs and milk will form an emulsion that helps to trap air and create the light, fluffy texture we’re used to. 

muffins in a pan with hands holding edges

Don’t Overmix. We know it can be tempting to continue to stir your batter once the ingredients are combined, but just trust us, okay? Doing so will only result in dense, thick muffins. Instead, stop mixing as soon as the ingredients are combined. 

Don’t Overbake. It’s likely that these muffins will be done baking before they look completely finished. So, be sure to test them with a toothpick! 

Storage & Freezing Options

One of our favorite things about this recipe is that it’s perfect for meal prep! Once baked, they can be stored for a long time, making them great for busy weeks. However, you might need to hide them from the rest of your family to do so, because they tend to go fast! 

Fridge: Store leftover muffins in an airtight container in the fridge for 1-2 weeks. 

Freezer: For longer-lasting protein muffins, place them in an airtight container or sealable bag in the freezer for up to 4 months! 

Prep

More Magnificent Muffins

If like us you can’t get enough muffins in your life you’re definitely going to want to check out a few more of our favorites! 

  • Honey sweetened and rich in protein, fiber, and calcium, flourless honey oat ricotta muffins are easy to make for a healthy breakfast or snack! 
  • Delicious, easy to make, and naturally sweetened, spiced pear muffins with nut topping are irresistibly delicious. 
  • Breakfast muffins with no added sugar are paleo-friendly for a great grab-n-go option!
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Chocolate chip Muffins in muffin pan. Sitting on cooling wrack. Two muffins out of pan and one with bite taken out. Spoon of sugar above pan

Flourless Chocolate Chip Protein Muffins


★★★★★

4.8 from 15 reviews

  • Author: Lindsay Cotter
  • Total Time: 30
  • Yield: 10–12 muffins 1x
  • Diet: Gluten Free
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Description

High protein, gluten free, low sugar, flourless, and delicious, these chocolate chip protein muffins are everything you ever wanted in a recipe and so much more! Make them ahead of time for a quick breakfast or on-the-go snack.


Ingredients

Units Scale
  • 2 cups gluten free rolled oats (192 -195 grams) – See notes if using gluten free oat flour.
  • ¼ cup (~60 grams) vanilla or chocolate vegan protein
  • 2 teaspoons baking powder
  • 1//2 teaspoon baking soda
  • ¼ teaspoon of salt
  • ¼ cup natural creamy nut butter or seed butter (no stir)
  • ½ cup maple syrup/honey
  • ⅔ cup non dairy milk
  • 2 eggs (room temperature) – or egg replacer. See notes.
  • 1 teaspoon vanilla extract
  • ½ cup dairy free dark chocolate chips or sugar free chocolate chips

Instructions

 

  1. Preheat the oven to 350° Fahrenheit. Line or grease a muffin tin; set aside.
  2. Place the oats in a high-powered blender, and grind until a flour-like texture is formed. Around 30 – 45 seconds.
  3. In a large bowl, whisk together the ground oats or oat flour, protein powder, baking powder, baking soda, and salt making sure to remove any flour clumps.
  4. In a separate large bowl, mix together the nut butter and maple syrup or honey until creamy. Set aside. *Note –  This bowl will be used to combine all of the ingredients.
  5. In a large liquid measuring cup, whisk together the milk, egg, and vanilla.
  6. Working in batches (as seen in the video below), combine ⅓ of the dry batter and ⅓ of the milk batter into the bowl of nut butter/syrup.
  7. Mix and repeat until all of the batters are combined and a cake-like texture is formed. Fold in the chocolate chips.
  8. Spoon the batter into the lined muffin pans, filling ⅔ of the way full. Place the muffin tin in the oven for 18-22 minutes or until the center comes out clean with a toothpick.
  9. Place the muffins on a cooling rack for 10 minutes before serving.
  10. Store in the fridge for up to 1-2 weeks or in the freezer for 4 months.

Notes

If using oat flour instead of oats, measure the weight of flour to match the oats (around 195 grams = a little under 2 cups)

For a nut free option use no stir sunflower seed butter. For egg free option, replace 2 eggs with ½ c mashed banana. Mash the banana with the nut butter batter. Texture and baking time will vary.

  • Prep Time: 10
  • Cook Time: 20
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American

Nutrition

  • Calories: 208
  • Sugar: 13.1
  • Sodium: 212.9
  • Fat: 7.2
  • Saturated Fat: 2.4
  • Carbohydrates: 28.3
  • Fiber: 4.3
  • Protein: 7.5
  • Cholesterol: 33.8

Keywords: gluten free, dairy free, protein muffins, flourless, muffins, healthy, breakfast

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Categories: Breakfasts, Dairy-Free, Gluten-Free, Has Video, Oven, Snacks and Appetizers, Vegetarian Tags: breakfast, egg free option, flourless, gluten free muffins, kid friendly, muffins, protein powder, snack, vegan option

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Lindsay Cotter of Cotter Crunch

About Lindsay

Hi, y’all, I’m Lindsay Cotter, a Nutrition Specialist with a focus on Gluten-Free eating. I love creating delicious nourishing food that anyone can enjoy.

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  1. Jules

    03/12/2023 at 2:45 PM

    Hello! I’m also confused by the grams given for the protein powder. I have 4 types of vegan vanilla protein powder and they’re all around 100-110 grams per cup. You have 60 grams for 1/4 cup. So that’d be 240 grams. Even if I really, really packed a 1/4-cup measuring cup, I wouldn’t get anywhere near 60 grams. Did that number perhaps come from metric conversion software? When you baked these, did you use a measuring cup or grams? So I know which measurement I should go with. Thank you! 🙂 I hope to make these tomorrow!

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      03/12/2023 at 6:27 PM

      Hi Jules! Just tried to email you. What type of protein powder are using. Most of my plant based protein powders come with a 2-4 tbsp scooper. 2 tbsp around 25 grams to 30 grams. Or a sample packet around 30 grams. But I don’t want this to cause any confusion so I can remeasure and report back.

      Reply
  2. Elizabeth Era Hens

    01/10/2023 at 6:20 AM

    is the nutrition facts for 1 muffin?

    ★★★★

    Reply
    • Avatar photoLindsay Cotter

      01/11/2023 at 12:54 AM

      Correct! Unless you use a sugar substitute

      Reply
  3. Analise

    12/22/2022 at 10:54 AM

    We loved these muffins! Amazing texture and easy to make! The chocolate chips did sink to the bottom for us.

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      12/22/2022 at 5:07 PM

      I’m so glad! Thanks for reporting back Analise! And what type of chocolate chips did you use?

      Reply
  4. Kas

    10/30/2022 at 8:13 AM

    These are delicious 😋 I substituted the oats for Millet flour as I have a ridiculous amount of intolerances now😭. They looked beautiful too! But…nothing compares to your work 💕 Thank you for all that you do and the endless creativity you present…

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      10/31/2022 at 4:52 PM

      Oh I love millet flour! Definitely try that next kas!

      Reply
  5. K_D

    08/19/2022 at 12:54 PM

    I typically hate it when people do this but wanted to share how I *mostly* followed this recipe and still got amazing results.

    We were very low on food and needed to do a shop but my husband still needed breakfast in the morning so I worked with what I had.

    We had cows milk, one egg and peanut butter with sugar in it but it still worked great. I substituted half a mashed banana for the other egg, put in 1/4 cup of maple syrup instead of the 1/2 cup due to the sugar in the peanut butter already and put the same amount of milk in as directed. (Oh and my husband prefers walnuts to chocolate chips so I made that change as well. )

    Do I think they could have been better if I followed the recipe exactly, for sure, but honestly they were a quick and easy breakfast made with what we had left in the house.

    Thanks for the recipe! It saved our Friday morning 🙂

    ★★★★

    Reply
    • Avatar photoShyanne

      08/19/2022 at 1:09 PM

      Thank you so much for telling us! We’re so happy to hear they worked well with your adjustments (and that your husband was able to have breakfast)!

      Reply
  6. Julia

    08/14/2022 at 7:38 PM

    Do you think this would work with powdered egg whites instead of protein powder?

    Reply
    • Avatar photoShyanne

      08/15/2022 at 3:48 PM

      Hi Julia!
      It should work just fine. However, the texture will likely be a bit lighter, and the baking time will differ. So, be sure to keep an eye on them in the oven. Please let us know how it goes if you give it a try!

      Reply
  7. Leah

    08/08/2022 at 8:07 AM

    Very sticky batter. The tops got a bit browned and crunchy, so I baked for only 15 minutes. These taste amazing, like a big oatmeal chocolate chip cookie!

    ★★★★

    Reply
    • Leah

      08/08/2022 at 8:39 AM

      I just realized I forgot to add the milk 🤦‍♀️. I’m sure that would’ve made a difference to the batter texture and muffin top and baking time! Sigh… next time…

      Reply
      • Avatar photoLindsay Cotter

        08/08/2022 at 10:35 AM

        Oh no! Yes that’s crucial. 🙊 was there something confusing in the recipe card that made you miss the milk? Let us know!

        Reply
        • Leah

          08/29/2022 at 6:17 PM

          Made the muffins again and this time remembered the milk! They turned out amazing with perfect muffin tops, nicely cracked. Great recipe 👍

          ★★★★★

          Reply
  8. Alexandra Warner

    03/03/2021 at 7:05 PM

    Can I replace the peanut butter with coconut oil?

    Reply
    • Alexandra

      03/04/2021 at 9:36 AM

      I ended using coconut butter! Will see how they turn out! Also used plant based blueberry muffin protein and replaced the chocolate chips with wild blueberries.

      Reply
      • Avatar photoLindsay Cotter

        03/04/2021 at 10:05 AM

        Sorry for the delay! Let me know how it turns out. I am not sure coconut butter will give the same texture but with a shot! Can you have almond butter or another seed butter?

        Reply
        • Alexandra

          03/04/2021 at 1:11 PM

          It turned out amazing with the coconut butter and the blueberry muffin protein made it so yum! I can have peanut butter but since I was making it like a blueberry muffin I didn’t want it to have a peanut flavor. As for the almond butter I just ran out!

          Reply
          • Avatar photoLindsay Cotter

            03/05/2021 at 12:32 PM

            woohoo! so glad!

  9. Vusala Aranjo

    02/07/2021 at 6:09 PM

    Wow – these turned out amazing. I have had so many disasters baking with similar ingredients, and I’m a pretty decent baker. This recipe is wonderful. I did add another scoop of whey protein powder, and instead of half a cup of honey, I did 1/4 lakanto and 1/4 honey. Thank you!

    Please post other baked protein and gluten free recipes!

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      02/08/2021 at 12:34 PM

      Thank you for your feedback and I’m so happy to hear tha tthe muffins were a success! We have plenty of other gluten free protein baked goods that you might enjoy, too. Lots of protein bites! Try the salted caramel snickerdoodle protein bites first. They’re delicious!

      Reply
  10. Kait

    02/07/2021 at 1:28 PM

    Subbed in some hemp protein and used cashew butter and these came out SO tasty. Excited to have them as a hearty snack throughout the week.

    Only thing is I didn’t get that perfect dome muffin top – mine are flat with a beautiful crack – if they were a bread, they’d be PERFECT! Thankfully looks don’t affect flavor. 😉

    Reply
    • Avatar photoLindsay Cotter

      02/07/2021 at 4:29 PM

      So glad! The dome usually come from the reaction to the baking soda/baking powder (make sure they are not expired), undermixing, or the heat of the oven. Either way, glad they are tasty!

      Reply
  11. Haylee Jane Monteiro

    01/29/2021 at 12:33 AM

    Hi Lindsay! I love the rise on these muffins and was hoping to try a variation this weekend

    Regarding the protein powder quantity, you mentioned 1/4 cup (~60 gr).
    1/4 cup of my protein powder is actually about 22 grams
    So for 60 g I would use 2 scoops (⅔ cup). I use the one from Quest Nutrition.

    Which one of these seems more right?

    Reply
    • Avatar photoLindsay Cotter

      01/29/2021 at 8:25 AM

      Hi Haylee! I would use the gram weight for the best accuracy.

      Reply
    • Avatar photoLindsay Cotter

      01/29/2021 at 11:56 AM

      By the way, are you using quest whey? If so, it will definitely be a lighter texture/weight than plant based protein. But will work great! Be sure to check baking times. Whey might bake faster. Hope this helps.

      Reply
      • Haylee Monteiro

        01/30/2021 at 10:27 PM

        Thanks so much for the quick response Lindsay!
        Yes, Quest is a whey-caesin blend. I typically do the same baking time when I use that, but reduce the oven temperature to 325 and it works perfectly.

        I’m going to put this one next on my list because it turned out more of my audience wanted a banana protein muffin as compared to an oatmeal protein muffin.

        I still do want to try this one though, and I’ll definitely link your page for inspiration credit when I try it!

        Reply
        • Avatar photoLindsay Cotter

          01/31/2021 at 2:23 PM

          Sounds good! Definitely keep me posted if you do end up making them with Quest.

          Reply
  12. Sonja Forrester

    01/03/2021 at 11:33 AM

    These taste great. Not sure what I did wrong. Maybe my protein I used. But the muffins seemed really liquidy when I placed in muffin pan but when cooked seemed too grainy or powdery. The muffin tops were great the rest of the muffins just crumbled apart. But my son still ate them with a spoon and a glass of milk. I will keep trying. Thanks for the recipe!

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      01/03/2021 at 10:25 PM

      Oh no! What protein powder did you use? It definitely could be that. Happy to help remedy this!

      Reply
      • Sonja Forrester

        07/17/2021 at 3:34 PM

        I used Organic protein powder. Just made again forgetting this happened and one muffin pan did this against and one stayed together. Maybe I over baked. I baked 20 mins.

        Reply
        • Avatar photoLindsay Cotter

          07/17/2021 at 3:59 PM

          Hi Sonja! What type of protein powder did you use? Is your baking soda/powder fresh? What setting on your oven? Is your oven older or newer? This will help me figure out what went wrong. Thanks!

          Reply
  13. Tammy

    10/18/2020 at 1:14 PM

    These are so yummy. I made two substitutions based on what I had on hand. I didn’t have honey, so I dissolved 1/2 cup of Swerve Granular Sweetener in hot water. I also used Optimum Nutrition Gold Standard 100% Whey Protein Powder in Double Rich Chocolate in lieu of vegan protein. The oat flour is so tasty and filling and a great alternative to flour.

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      10/20/2020 at 8:14 PM

      Glad those substitutions worked out for you!

      Reply
  14. Katie

    05/19/2020 at 3:14 PM

    The use of oats is brilliant in these muffins- adds texture and makes these muffins that much better!

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      05/21/2020 at 6:54 PM

      Thank you, Katie!

      Reply
  15. Suzy

    05/13/2020 at 10:56 AM

    LOVED them! Just perfect for when I didn’t have any flour in the house but really wanted a muffin!

    ★★★★★

    Reply
  16. Leigh Ann

    05/13/2020 at 7:36 AM

    These muffins looks incredible! Love that they are flourless too!

    Reply
  17. Natasha

    05/12/2020 at 7:45 PM

    I would love one for breakfast!!

    Reply
  18. Alice Choi

    05/12/2020 at 5:03 PM

    love these chocolate chip protein muffins!!

    Reply
  19. Jodi

    05/12/2020 at 11:23 AM

    I love the idea of a protein muffin, but what can I sub for the oatmeal to reduce the carbs? The serving nutritional breakdown is for 11 muffins, but the recipe makes 12? Thank you.

    Reply
    • Avatar photoLindsay Cotter

      05/12/2020 at 11:32 AM

      Hi there! sorry yes, it’s for 11 because you can make anywhere between 10-12 muffins. It just depends on how much you fill the muffins pan. I filled them 2/3 full so it made 10 versus if you fill half way it will make 12. Hope that makes sense.

      Not sure what you could substitute for oats. What do you have on hand? maybe a low carb cereal? I think coconut flour would be too dry. Maybe oat bran ?

      Reply
  20. Toni

    05/12/2020 at 5:43 AM

    Everyone at my house loved it! So good and delish!

    ★★★★★

    Reply
  21. Lauren k

    05/11/2020 at 10:12 AM

    What a delicious way to add more protein! I love your recipes!

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      05/11/2020 at 6:37 PM

      Thanks, Lauren!

      Reply
  22. Cara

    05/11/2020 at 6:38 AM

    In the oven as I type. Made the recipe as is, but put it in a 7×11 pan instead.
    So excited.

    ★★★★★

    Reply
    • Avatar photoLindsay Cotter

      05/11/2020 at 10:10 AM

      I’m so glad it worked out! YAY!

      Reply

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Flourless Chocolate Chip Protein Muffins Pinterest Image
muffins in a pan with hands holding edges
Lindsay Cotter of Cotter Crunch

About Lindsay

Hi, y’all, I’m Lindsay Cotter, a Nutrition Specialist with a focus on Gluten-Free eating. I love creating delicious nourishing food that anyone can enjoy.

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