These Gluten-Free Chocolate Chip Protein Muffins will become your new favorite breakfast or grab-n-go snack. 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.
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!
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!
Tips & 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.
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!
Chocolate Chip Protein Muffin Ingredients
For these protein muffins, we kept standard baking ingredients like salt, vanilla extract, and baking soda but gave everything else a nutrient-rich upgrade!
- 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.
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.
How to Make Chocolate Chip Protein Muffins
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.
- Preheat the oven to 350° Fahrenheit, and add muffin liners to your favorite muffin pan. Or, grease it with a high-quality cooking spray.
- Pulse the oats in a blender until a flour-like consistency is formed.
- Whisk the dry ingredients together in a large mixing bowl until smooth.
- Then, in a separate large bowl, combine the nut butter and maple syrup (or honey) until they are smooth and creamy.
- 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.
- Repeat the process until all of the ingredients have been combined and a cake-like batter is formed.
- To finish, fold in the chocolate chips, and spoon the batter into the muffin pan.
- Bake until the center of your muffins comes out clean with a toothpick. Important Note: The baking time may vary based on the type of protein powder used so be sure to check baking progress starting at 12-15 minutes.
- Let them cool completely on a wire rack on the counter before serving.
Stand Mixer Instructions
For a more hands-off recipe, we also tested these muffins with a hand mixer! Here’s what to do:
- Beat the nut butter and maple syrup with a paddle attachment.
- 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!
- Spoon the batter into the prepared muffin pan, and bake at 350° Fahrenheit for 16-22 minutes. Remove them from the oven, and let your muffins cool completely before serving.
What Protein Powder to Use
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.
In addition, it yields the best texture creating light and fluffy muffins instead of dense and grainy ones.
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!
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!
More of Our Favorite
Gluten-Free Muffin Recipes
- 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!
Gluten-Free Chocolate Chip Protein Muffin Recipe
- Total Time: 30
- Yield: 10–12 muffins 1x
- Diet: Gluten Free
Description
High protein, gluten-free, low sugar, flourless, and delicious, these chocolate chip protein muffins can be made ahead of time for a quick breakfast or on-the-go snack.
Ingredients
- 2 cups gluten-free rolled oats (192 -195 grams) – See notes if using gluten-free oat flour.
- ¼ cup (or 30 – 40 grams) vanilla or chocolate vegan protein *grams per ¼ cup will vary depending on the brand of protein powder.
- 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 to ¾ cup non-dairy milk (see notes)
- 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
- Preheat the oven to 350° Fahrenheit. Line or grease a muffin tin; set aside.
- Place the oats in a high-powered blender, and grind until a flour-like texture is formed. Around 30 – 45 seconds.
- 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.
- 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.
- In a large liquid measuring cup, whisk together the milk, egg, and vanilla.
- 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.
- Mix and repeat until all of the batters are combined and a cake-like texture is formed.* Fold in the chocolate chips.
- Spoon the batter into the lined muffin pans, filling ⅔ of the way full. Place the muffin tin in the oven for 16-22 minutes or until the center comes out clean with a toothpick. Important Note: Check the muffins after 15 minutes of baking, as the baking time may vary based on the type of protein powder used.
- Place the muffins on a cooling rack for 10 minutes before serving.
- Store in the fridge for up to 1-2 weeks or in the freezer for 4 months.
Notes
Protein powder tip: This recipe was tested with plant-based protein powder (pea/rice blend). Whey protein tends to hold more moisture, which can make the muffins sticky or gummy. If you’d like to use whey, try either reducing the milk by 1–2 tablespoon or adding 1–2 tablespoons more oat flour to help balance moisture.
Baking Tips – If you are using oat flour instead of oats, measure the weight of flour to match the oats (around 195 grams = a little under 2 cups) If you’re protein powder tends to be on the thicker side when mixed, use ¾ cup milk.
Substitutes – 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
Hi Lindsey,
I was starting to measure things for trying out your muffins. And when I went to measure the protein powder, if I understand it correctly you said a quarter cup or around 60 g. but when I measure out a quarter cup of protein powder, and check it on my scale, it comes out to 16 g. Could you please clarify for me before I try the recipe? it sounds like it might be very good.
Thanks so much.
Hi CLM! Thanks for catching that. The weight in grams can definitely vary depending on the brand and type of protein powder. Most vegan protein powders are closer to 25–30 grams for 1/4 cup, not 60 grams, so I’ll be updating the recipe card to reflect that. I’d stick with the 1/4 cup measurement for now—it’ll still work, but the protein count may vary depending on your powder.
These came out amazing! I used the Bob’s red mill vegan egg replacer and it worked perfectly too.
Have you ever tried this recipe as a bread? Do you think anything would need to be altered if I tried this recipe as a bread?
Hi Megan! I haven’t tried making it into a bread but it’s worth a shot! I’m not sure of the exact baking times or outcome of the texture but I would start checking bread around 30 minutes for doneness. It could take up to 45 minutes. Keep me posted!
Is there a sugar free alternative that I can use in place of the maple syrup/honey?
Hi Jan! I’ve used lakanto maple syrup before. There syrup is the closest I’ve gotten to real maple syrup without the sugar. https://www.lakanto.com/products/lakanto-maple-flavored-syrup-bottle-13-fl-oz
What brand of protein powder do you use? I’m on the look out for a new one! And I can’t wait to try these 🙂
Are you looking for a plant based protein? The peanut butter or vanilla KOS works well with this recipe! I have a discount code if you want to use it! https://glnk.io/wnyxl/cottercrunch COTTERCRUNCH 15% off
My family loved these muffins! My kids usually get a lil “scared” when I make a recipe without added refined sugar or all purpose flour. They all had two thumbs up for the sweetness factor! We will definitely have these muffins in our rotation.
Woohoo! So glad to hear it, Celena. Thanks for making our day! Happy baking!
Any reason one couldn’t use regular dairy milk in these? Thanks!
Hey Sonya! Regular dairy milk will work just fine in these muffins. Enjoy!
Hi! Love these…but there is now an oat/oat flour shortage…Any other gf fours that might work?
Just emailed you! Wow I hadn’t heard that. I do have a recipe for Millet flour in my new cookbook that would work. It’s easy to make too!
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!
Hi Jules! Just tried to email you. Thanks for catching that. The weight in grams can definitely vary depending on the brand and type of protein powder. Most vegan protein powders are closer to 25–30 grams for 1/4 cup, not 60 grams, so I’ll be updating the recipe card to reflect that.
is the nutrition facts for 1 muffin?
Correct! Unless you use a sugar substitute
We loved these muffins! Amazing texture and easy to make! The chocolate chips did sink to the bottom for us.
I’m so glad! Thanks for reporting back Analise! And what type of chocolate chips did you use?
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…
Oh I love millet flour! Definitely try that next kas!
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 🙂
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)!
Do you think this would work with powdered egg whites instead of protein powder?
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!
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!
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…
Oh no! Yes that’s crucial. 🙊 was there something confusing in the recipe card that made you miss the milk? Let us know!
Made the muffins again and this time remembered the milk! They turned out amazing with perfect muffin tops, nicely cracked. Great recipe 👍
Can I replace the peanut butter with coconut oil?
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.
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?
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!
woohoo! so glad!
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!
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!
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. 😉
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!
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?
Hi Haylee! I would use the gram weight for the best accuracy.
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.
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!
Sounds good! Definitely keep me posted if you do end up making them with Quest.
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!
Oh no! What protein powder did you use? It definitely could be that. Happy to help remedy this!
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.
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!
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.
Glad those substitutions worked out for you!
The use of oats is brilliant in these muffins- adds texture and makes these muffins that much better!
Thank you, Katie!
LOVED them! Just perfect for when I didn’t have any flour in the house but really wanted a muffin!
These muffins looks incredible! Love that they are flourless too!
I would love one for breakfast!!
love these chocolate chip protein muffins!!
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.
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 ?
Everyone at my house loved it! So good and delish!
What a delicious way to add more protein! I love your recipes!
Thanks, Lauren!
In the oven as I type. Made the recipe as is, but put it in a 7×11 pan instead.
So excited.
I’m so glad it worked out! YAY!