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I love making these chocolate chunk protein muffins. They always come out soft, chocolatey, and full of flavor. They’re perfect for breakfast on the go, a snack between meals, or even a sweet treat that doesn’t leave you feeling guilty. These muffins are packed with wholesome ingredients like oats, cottage cheese, and eggs, and each bite gives you a good amount of protein, fiber, and chocolatey goodness.

Chocolate chunk protein muffins in a muffin tin.

Chocolate Chunk Cottage Cheese Muffins are the Best

You can have these chocolate chunk cottage cheese muffins for breakfast, an afternoon snack, or after-dinner dessert. They’re versatile enough to work in any scenario.

These cottage cheese muffins are soft and fluffy with a hint of cinnamon and just the right amount of chocolate in every bite. Blended until smooth and then baked to golden perfection in under 20 minutes. Thanks to the cottage cheese and eggs, they’re naturally high in protein, and the oats give them that satisfying muffin texture—no flour needed!

Not only that, but these muffins are perfect for meal prepping for the week!

If you love cottage cheese to add protein to your recipes, check out all of my favorite cottage cheese recipes. The cottage cheese chocolate mousse is a favorite!

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Hand holding a chocolate chunk muffin out of the muffin tin.
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Recipe Ingredients

  • Old Fashioned Rolled Oats – Gluten free rolled oats work great and become the base when blended into the batter. They add fiber and structure.
  • Eggs – Help bind everything together and add protein.
  • Baking Powder – Gives these muffins lift and fluffiness.
  • Cinnamon – Adds a cozy, warm flavor that pairs perfectly with the banana and chocolate.
  • Cottage Cheese – Use full-fat or low-fat; it makes the muffins moist and creamy while bumping up the protein content.
  • Honey – Naturally sweetens the muffins without refined sugar.
  • Chocolate Chunks – Add rich cocoa flavor to every bite. You can sub mini chocolate chips if you prefer.
Ingredients for chocolate chunk cottage cheese muffins measured and labeled.

Variations

  • Swap chocolate chunks for chocolate nibs, mini chocolate chips, or add in chopped walnuts.
  • Add a scoop of vanilla protein powder if you want an even bigger protein boost.
  • Replace honey with maple syrup or agave if that’s what you have on hand.
  • Fold in mashed ripe banana (½ to 1 banana) for a stronger banana flavor and extra moisture.

How to Make Cottage Cheese Muffins with Chocolate Chunks

Ingredients added to a food processor.
  1. Preheat the oven to 350°F (175°C) and lightly grease or line a muffin tin. Add the cottage cheese, oats, honey, eggs, baking powder, and cinnamon to a high powered blender for a smoother batter, or a food processor.
Ingredients blended together in a food processor.
  1. Blend until the batter is smooth and thick, scraping down the sides as needed.
Batter in a bowl with chocolate chunks.
  1. Pour the batter into a bowl and gently fold in the chocolate chunks.
Batter scooped into a muffin tin.
  1. Scoop about 1½ tablespoons of batter into each muffin cavity. Top with extra chocolate if you’d like.
Cottage cheese chocolate chunk muffins fully cooked in a muffin tin.
  1. Bake in the preheated oven for 15-18 minutes, or until the tops are set and a toothpick comes out clean.
Hand holding a cottage cheese muffin with chocolate chunks.
  1. Let them cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.

Tips for Cottage Cheese Muffins

  • Use a high-powered blender for a smoother batter – This helps break down the oats and create a smoother batter.
  • Don’t overbake – Keep an eye on the muffins after 15 minutes so they stay soft and tender.
  • Let them cool completely – This helps them firm up and makes them easier to remove from the muffin tin.
  • Store in the fridge – Because they’re made with cottage cheese, these muffins keep best in the fridge and will last up to 5 days.
Close up of cottage cheese chocolate chunk protein muffins.

Protein Muffin Variations

  • Blueberry protein muffins – Replace chocolate with fresh or frozen blueberries.
  • Peanut butter swirl – Add a teaspoon of peanut butter on top of each muffin before baking and swirl with a toothpick.
  • Chunky monkey – Add mashed banana, walnuts, and a sprinkle of coconut flakes.
Close up of hand holding a protein muffin.

Recipe FAQs

Are these cottage cheese muffins gluten-free?

Yes! As long as you use certified gluten-free oats, these muffins are naturally gluten-free.

Can I freeze cottage cheese muffins?

Absolutely. Once they’ve cooled, place them in a freezer-safe bag or container. They’ll last up to 3 months. Just thaw overnight or warm in the microwave for 30 seconds.

What kind of cottage cheese works best?

I recommend using 2% or full-fat cottage cheese for the creamiest texture and best flavor. If you prefer low-fat, it still works, but the muffins may be a little less rich.

Can I add protein powder?

Yes! A scoop of vanilla or unflavored protein powder can be added to the batter. If the batter becomes too thick, add a splash of milk to loosen it up.

How do I store cottage cheese muffins?

Store your muffins in an airtight container in the refrigerator for up to 5 days. These are perfect for meal prep—grab one in the morning and you’re out the door with a healthy breakfast in hand.

Close up of cottage cheese muffins with chocolate chunks on a plate.

These chocolate chunk protein muffins are gluten free, high protein, and a quick recipe made in less than 30 minutes. Perfect for meal prep! Your only problem will be deciding when to have them: breakfast, snack time, or for dessert! Either way they are a HIT!

If you enjoyed this recipe, please consider leaving a STAR ⭐️ RATING in the COMMENTS 📝 SECTION below.

Choco
5 from 2 votes
Servings: 12

Chocolate Chunk Protein Muffins

By JENNIFER GAMBLE
These chocolate chunk protein muffins are made with cottage cheese, eggs, and oats. They are gluten-free and full of fiber and protein.
Prep: 5 minutes
Cook: 18 minutes
Total: 23 minutes
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Equipment

  • 1 food processor

Ingredients 

  • 1 1/2 cups Gluten-free old-fashioned rolled oats
  • 225 grams cottage cheese
  • 2 eggs
  • 2 teaspoons baking powder
  • 1 teaspoon cinnamon
  • 1/4 cup honey
  • 1/2 cup chocolate chunks

Instructions 

  • Preheat the oven to 350°F (175°C) and lightly grease or line a muffin tin.
  • Add the 225 grams cottage cheese, 1 1/2 cups Gluten-free old-fashioned rolled oats, 1/4 cup honey, 2 eggs, 2 teaspoons baking powder, and 1 teaspoon cinnamon to a high powered blender for a smoother batter, or a food processor.
    Cottage cheese, eggs, oats, honey, cinnamon, and making powder in the food processor.
  • Blend until the batter is smooth and thick, scraping down the sides as needed.
    Batter in the food processor.
  • Pour the batter into a bowl and gently fold in 1/2 cup chocolate chunks.
    Chocolate chunks folded into the muffin batter.
  • Scoop about 1½ tablespoons of batter into each muffin cavity. Top with extra chocolate if you’d like.
    Muffin tin with muffin batter.
  • Bake in the preheated oven for 15-18 minutes, or until the tops are set and a toothpick comes out clean.
    Fully cooked cottage cheese muffins with chocolate chunks.
  • Let them cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.
    Close up of chocolate chunk protein muffins.

Notes

Each muffin has about 7g of protein and 4g of fiber! 
Substitute chocolate chunks for chocolate chips or your other favorite additions.
Store in an airtight container in the refrigerator for 4-5 days. Perfect for meal prep! 
Use a high-powered blender for a smoother batter. I used a food processor with this recipe because I love the thicker texture with the chocolate chunks.

Nutrition

Calories: 204kcal, Carbohydrates: 31g, Protein: 7g, Fat: 6g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 0.01g, Cholesterol: 31mg, Sodium: 143mg, Potassium: 181mg, Fiber: 4g, Sugar: 9g, Vitamin A: 70IU, Vitamin C: 0.04mg, Calcium: 81mg, Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Like this? Leave a comment below!


JENNIFER GAMBLE

Hello! I’m Jennifer, but you can call me Jen. I’m a wife and mom, cook, recipe developer, nutrition coach, and food photographer.

With a formal certification in nutrition and over a decade of hands-on experience in the online food industry, I bring a well-rounded perspective to all of the recipes here on Simply Macros.

As the creator and author, I ensure that every recipe not only looks visually appealing but is also grounded in sound nutritional principles.

I hope you enjoy these recipes as much as I enjoyed creating them.

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Recipe Rating




3 Comments

  1. Anon from MD says:

    5 stars
    Becuase of the high-FODMAP content of honey, I swapped out the honey for maple syrup. These were very good. Thank you.

    1. JENNIFER GAMBLE says:

      Yay! Great substitute, and I am glad you enjoyed them.

  2. JENNIFER GAMBLE says:

    5 stars
    These are so good! My favorite way to eat them is for breakfast. Just pop them in the microwave for 20 seconds, and they are perfect. It’s an easy breakfast prep for the week.