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Home » Recipes » Baking

Chocolate Chip Protein Muffins

Published: Jan 29, 2026 by Danika Vanderpyl · This post may contain affiliate links · Leave a Comment

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I make protein chocolate chip muffins on repeat these days as I just had my third baby, and I find muffins are a must when we don't have two hands free (ahem, breastfeeding, holding a child)! These delicious muffins are high in protein (9 grams per muffin) from the almond flour and the cottage cheese; no protein powder is needed to make these.

A basket with a tea towel with muffins that have chocolate chips on top/

I'm a huge fan of recipes with chocolate chips (like these whole-wheat chocolate chip cookies and whole-wheat chocolate chip muffins). When I had the idea to make high-protein muffins, I wanted to see if I could make them with cottage cheese and almond flour, and without protein powder. They are also gluten free. I didn't want chunks of cottage cheese, so it was important to make these in the blender, and after a few tests, they turned out delicious. I even gobbled down three at once when testing them...

Jump to:
  • Ingredients needed
  • Danika's insight on homemade muffins
  • How to make gluten-free, protein-dense, chocolate chip muffins
  • Tips for the best homemade flourless muffins
  • More protein recipes to try
  • Chocolate Chip Protein Muffins
  • Danika Vanderpyl, C.H.N

Ingredients needed

Butter, cottage cheese, chocolate chips, vanilla, almond flour, coconut sugar, baking powder, eggs in bowls.

Danika's insight on homemade muffins

As someone who studied nutrition for 2 years and continues to choose to feed my family with whole foods, I want to encourage you!

It's a huge win that you are choosing to make muffins at home. Let's all realize muffins from the store are completely different than a homemade muffin! We don't have any preservatives, and we choose ingredients that are actually nutrient-dense, contributing to your well-being.

So keep crushing it and make the homemade muffins! ❤️ On my blog, I only share healthy snacks, so you will find all the healthy muffin recipes I make for my family on repeat.

How to make gluten-free, protein-dense, chocolate chip muffins

These step-by-step photos are from my kitchen. Follow along, and let's make some muffins!

A vitamix with ingredients for protein muffins.
  1. Preheat the oven to 425 degrees Fahrenheit (215 °C). In a blender container, add the eggs, vanilla, cottage cheese, melted butter, and coconut sugar, then pulse until everything is smooth and combined.
Blender with protein batter for muffins.
  1. The batter will look thin and consistent like the photo above. Now add the almond flour, baking powder, and chocolate chips. Pulse only for 10 seconds (so the chocolate chips don't get too crushed and the batter doesn't become too dense).
A vitamix with chocolate chip muffin batter and a spatula beside it.
  1. Use a spatula to scrape down any flour that wasn't mixed in, and fold any other dry bits of flour into the mix. Place muffin liners into a muffin pan. Fill each muffin cup all the way up - about ⅓ cup each.
Chocolate chip muffin batter in paper muffin liners in a pan.
  1. Sprinkle the top of the muffins with chocolate chips. Place the muffin tin in the preheated oven (425 degrees Fahrenheit or 215 °C) to bake for 8 minutes to help them rise, then turn the oven down to 375 degrees Fahrenheit (190 °C) and bake for another 8-10 minutes, until they are fully baked.

Tips for the best homemade flourless muffins

  • Do not overmix muffin batter! When making muffins, it's best to fold the batter together only until combined, which results in a more airy, fluffy muffin texture and a better crumb, rather than a dense, squat muffin when the batter is overmixed.
  • I think muffins look more appetizing or delicious when they have some kind of topping. In this case I put some chocolate chips on the top!
  • Let the muffins sit for 5 minutes before removing them from the pan. When muffins are still hot, they easily break; letting them cool slightly stops them from crumbling.
  • Use cupcake liners. With the almond flour, they have a thick texture that would be harder to come out of the pan without liners. I have used silicone liners or paper liners. I find that when the muffins are in a grease pan or with paper liners, they will bake 2-3 minutes faster than when they are in silicone liners.
  • Next try my other gluten free blackberry muffins.
A graphic of the snack prep pro e book.

I created an eCookbook for prepping snacks! This was designed to set aside a block of time weekly or monthly to batch prep wholesome snacks. They are freezer-friendly recipes, with a clear plan (grocery list too!) to make the most of a two-hour time block!

GRAB THE ECOOKBOOK!
Cottage cheese flourless protein muffins with chocolate chips on top.

More protein recipes to try

If you love chocolate chips like me, try this healthy edible cookie dough next, it's one of my favorite snacks and it's also made of whole food ingredients that are higher in protein!

  • Chocolate covered ice cream bars dipped in nuts.
    Chocolate Covered Ice Cream Bars (Healthy Dairy-Free Recipe)
  • Brown banana protein muffins with chocolate chips sitting on a cooling rack beside a plate of chocolate chip muffins.
    Protein Banana Muffins with Oats
  • A chunk of granola with oats and hemp hearts.
    Hemp Granola
  • A brown muffins with green flecks on a cutting board.
    Healthy Zucchini Muffins with Yogurt
See more High Protein →

💪🏼Did you make these protein chocolate chip muffins? Would you take 5 seconds to give a star rating and review just below the recipe? That means SOO much to me!! And it helps the growth of the Beside the Mountain blog. (Your email address will not be shown)

A basket with a tea towel with muffins that have chocolate chips on top/

Chocolate Chip Protein Muffins

Danika Vanderpyl
With 9 grams of protein, these chocolate chip muffins are perfect to energize your day. The almond flour makes this recipe high in protein and gluten-free.
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Prep Time 10 minutes mins
Cook Time 18 minutes mins
Total Time 28 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 10 muffins
Calories 294 kcal

Equipment

  • 1 muffin pan

Ingredients
  

Wet Ingredients

  • 3 eggs
  • 1 teaspoon vanilla
  • 1 cup cottage cheese
  • ¼ cup melted butter
  • ½ cup coconut sugar or brown sugar

Dry Ingredients

  • 2 cups almond flour
  • 1 ½ teaspoons baking powder
  • ⅔ cup chocolate chips + a few for on top

Instructions
 

  • Preheat the oven to 425 Fahrenheit (215 C). In a blender container, place eggs, vanilla, cottage cheese, melted butter, and coconut sugar. Pulse together for 30 seconds until well-mixed and the cottage cheese is fully blended.
  • Add the almond flour, baking powder, and chocolate chips. Blend for another 10 seconds until almost all combined. Use a spatula to scrape down the sides and stir in any flour that wasn't incorporated, but do not stir more than needed.
  • Put ⅓ cup of batter into paper liners - this makes about 10 muffins. Bake for 8 minutes at 425 Fahrenheit (215 C) and then lower the oven to 375 Fahrenheit (190 C) and bake for another 10 minutes. Let the muffins cool for 5 minutes before removing them from the pan.

Notes

Storage: These are fine on the counter for 1-2 days. If you want them to last longer, I recommend keeping them in the fridge to last for about 5 days. 
Freezing: These cottage cheese chocolate chip muffins freeze super well! Keep them in a bag or an airtight container and eat within 6 months. 

Nutrition

Serving: 1muffinCalories: 294kcalCarbohydrates: 20gProtein: 9gFat: 21gSaturated Fat: 7gPolyunsaturated Fat: 0.5gMonounsaturated Fat: 2gTrans Fat: 0.2gCholesterol: 65mgSodium: 201mgPotassium: 76mgFiber: 2gSugar: 14gVitamin A: 242IUCalcium: 117mgIron: 1mg
Keyword Chocolate chips, Cottage Cheese, Healthy Muffins, High Protein
Did you love this recipe?Make sure to leave a comment below!
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Danika Vanderpyl, C.H.N

I create snack recipes with healthy ingredients that are mostly already in your kitchen. I'm certified in Holistic Nutrition and I care about giving my kids real food. Let me share my nutrient-dense easy snacks with you.

Learn more about me →

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Danika-vanderpyl-hiking-with-mountains

Hey hey! I'm Danika.

I'm certified in holistic nutrition and I create snack recipes! Because unprocessed, wholesome, nutrient-dense snacks are hard to find but I want everyone to know they are easy to make!

About me

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