Soft, moist, and sweetened with chocolate chips! These chocolate chip protein muffins make the perfect snack. With 10 grams of protein per muffin and naturally gluten-free, these protein muffins will become an easy household staple.
These protein muffins have a cake-like texture right out of the oven without all the added sugar-y ingredients (just like these banana protein muffins!)
They’re easy to whip up (which means a great meal prep recipe to have on hand!) and have on hand for days you need something grab and go.
- Naturally gluten-free, dairy-free, soy-free, and grain-free
- 10 grams of protein per muffin (as a Certified Nutrition Coach this is huge to me!)
- Light and soft
- QUICK – toss everything in a bowl to mix and you’re pretty much done
- Use them as a healthy breakfast, a healthy snack, or a post-workout meal
- Kids can make them (they’re that easy!)
Ingredients You Need
If you have a good stock of gluten-free pantry staples, you’ll probably have everything you need to make this protein muffin recipe!
Almond flour: not to be mistaken for almond meal. Almond flour will help keep these high-protein muffins light and indulgent. Almost “cakey”. Learn more about the difference between almond flour and ground almonds.
Vegan protein powder: the kind of protein you choose will make a huge difference to the texture and the flavor of the chocolate chip protein muffins. For best results, use the vanilla protein from Genuine Health.
Baking powder: this does make them rise slightly.
Tapioca Flour: you don’t need a lot but it helps hold these muffins together and gives them so sustenance.
Non-dairy yogurt: this helps keep the muffins from becoming dense.
Mini chocolate chips: make sure to use allergy-friendly chocolate chips (I use Enjoy Life) and definitely opt for mini ones so that you get more in each bite!

How To Make Them
1. In a bowl, mix together the dry ingredients (except chocolate).
2. One by one add in the wet ingredients, saving the milk until last.
3. Mix until combined and fold in the chocolate chips.
4. Scoop into silicone muffin cups and bake!
5. Let cool in the pan.
Step By Step Photos




Choosing A Protein Powder
Not all protein powders are created equal and you cannot always sub powder for powder.
These protein muffins are made with Genuine Health’s Vanilla Protein. Genuine Health’s Fermented Vegan Protein Powder helps fuel your goals, recover and stay full. Made with 20 grams of plant-based protein, this vegan powder is dairy-free, gluten-free, non-GMO, and certified organic.
It’s also been voted one of the best tasting vegan powders. But best of all is that this protein is fermented. This helps break down the “anti-nutrient” in grains, nuts, seeds, and legumes that often causes bloating.
This protein literally gives you the best of both worlds.
Shop the Genuine Health Store on Amazon.

Important Teaching Tips
If you need to swap out the protein powder, another great option is Progressive Vanilla Protein Powder. It’s similar to Genuine Health in the way it absorbs. The batter for the muffins is pretty thick, you definitely need to portion it out manually versus “pour it”.
Because protein powders absorb differently, I don't think you can use whey protein powder for this recipe.
Any non-dairy yogurt should work for the protein muffin recipe. I’ve used both almond yogurt as well as coconut yogurt. Opt for unflavored. However, I’m not sure how dairy-free Greek yogurt would work as it’s much thicker.
Though you can’t substitute whey protein for vegan protein powder, you should be able to swap out flavors. For example: use chocolate protein powder for double chocolate protein muffins!
Frequently Asked Questions About Protein Muffins
Each protein powder will bake differently. Vegan protein absorbs much more liquid in a recipe (thanks to pea protein) than whey protein powder. Thus, they’re not always interchangeable. The best protein powders to use are pea protein, whey, or casein in either an unflavored or vanilla flavor.
It’s always best to use the protein specified in the recipe whenever possible.
High protein muffins should be stored in the fridge or freezer. They can be eaten right out of the fridge and taste delicious. Some muffins will firm up from the fridge slightly though. Chocolate chip protein muffins can also be stored in the freezer. Just pop one into the fridge the night before and let it thaw!
Maple syrup helps keep the muffins sweet without being too overbearing. Using granulated sugar won’t work as it will throw off the wet: dry ratio of the protein powder muffins and alter their texture. Likewise, honey is much thicker than maple syrup. So while it make work it will still alter them slightly.
Other Protein Recipes You'll Love
- Protein granola
- Oven baked protein oatmeal (make ahead breakfast!)
- Chocolate chip granola
- Blueberry protein muffins
- Flourless peanut butter protein muffins
- Make-ahead breakfast recipes
- Overnight cookie dough protein oats
- Chocolate chia protein balls
- Peanut butter and jam protein balls
- Chocolate fudge protein balls
- Crunchy granola
- Sugar-free granola
- Fudgy protein brownies
- Chocolate chip granola bars
- High protein cookies
- High protein pancakes
- Yogurt protein pancakes
- Energizing protein bar
- Easy, no-bake vanilla protein bar
- High protein snack recipes


Gluten-Free Protein Powder Muffin Recipe
Equipment
- Muffin tray
Ingredients
- ½ cup vegan protein powder
- 1 teaspoon baking powder
- ⅓ cup almond flour
- 1 tbs tapioca flour
- ¼ cup dairy free yogurt
- ⅛ cup maple syrup
- ¼ cup mini chocolate chips
- 1 egg
- ¼ cup non-dairy milk
Instructions
- Preheat the oven to 350 degrees Farenheit.
- In a baking bowl, combine the first four ingredients.
- One by one add in the wet ingredients and mix really well.
- Fold in the chocolate chips.
- Let sit for 2-3 minutes for the ingredients to absorb.
- Use a trigger ice cream scoop to portion the batter into muffin cups.
- Bake for 34 minutes. Remove from the oven and let cool fully in the pan.
Video
Notes
- The muffins taste best fresh or at room temperature. When stored in the fridge, let them sit at room temp before eating.
- The batter will be thick. You need to scoop it into the muffin tins (it won't pour). This is normal!
- Opt for silicone muffin cups if possible. The paper muffin cups won't peel off as easy.
- Any non-dairy yogurt should work. I’ve used both almond yogurt as well as coconut yogurt. Opt for unflavored. However, I’m not sure how dairy-free Greek yogurt would work as it’s much thicker. Though you can’t substitute whey protein for vegan protein, you should be able to swap out flavors. Peanut butter chocolate chip protein muffins would be delicious too!
- Grab all the ingredients from my Pantry Staples
Disclaimer:
Nutrition values are estimates only, using online calculators. Please verify using your own data"
Kelly
These muffins look so yummy. I just bought a bag of almond flour. Can't wait to try them!
fitasamamabear
Omg they're heaven lol the perfect combo of healthy and YUM lol
Glenda
It's hard for my brain to accept these as good for me because they're so delicious. lol. What a wonderful dilemma! Thanks for sharing your recipe!
fitasamamabear
Hhahaha that's the BEST kind of recipe!
Jenni
These muffins are so good! I wanted to eat them all in one sitting! I restrained myself, but I wanted to.
fitasamamabear
I totally ate four in my first sitting... so I feel yah!
Lisa
I'm always looking for new ways to up the protein in my favorite baked goods and this recipe delivered. So yum too!
fitasamamabear
Right?! It's nice to know you're indulging and getting some fuel!
Sherry
What a great recipe! I have been looking for more protein powder recipes and I hit the jack-pot when I found your website! Thank you for so many great recipe!!
fitasamamabear
Hehe Yay! This legit makes me happy haha there is so much goodness to be had!
Paula
I really have to work at getting enough protein and I love these muffins. They help me reach that goal as well as keep me fuller longer.
fitasamamabear
That they do! it's nice when something you want and something you need collide eh?
Jennifer
I love that these are lower in carbs and higher in protein! So easy and delish, too!
fitasamamabear
Plus easy to make 😉