Double Chocolate Chip Cottage Cheese Muffins

If you know me, then you know that I’m obsessed with all things cottage cheese. It’s just such a fantastic ingredient for adding to all kinds of different recipes to give them a big protein boost, and I’ve been so thrilled that regular readers have loved my blueberry cottage cheese muffins and banana cottage cheese muffins just as much as I do! 

Today I’m bringing you my latest creation, and they’re perfect for healthy snacking and when you need to get some extra protein. This time, we’ve got a beautiful, bakery style double chocolate chip creation, and I’ve added in a scoop of chocolatey protein powder so they come in at just 250 calories and an impressive 8 grams of protein each

They’re moist, perfectly sweet, loaded with chocolate flavor, and they look and taste just as good as your favorite store-bought muffin! They’re also freezer friendly and you can totally make them your own by adding in extras like chopped nuts. Enjoy! 

(Be sure that you don’t miss some of my most popular high protein, cottage cheese creations. I think you’ll also love my cottage cheese chocolate mousse, cottage cheese chocolate chip cookies, TikTok famous cottage cheese ground beef bowls, and cottage cheese pizza bowls!) 

chocolate cottage cheese muffins

Ingredients

  • All-purpose flour: Gives the muffins structure. 
  • Chocolate protein powder: Bumps up the protein, making these muffins more satisfying. Use your go-to whey, plant-based, or collagen protein—just know flavor and sweetness can vary.
  • Coconut sugar: Adds a deep, caramel-like sweetness without being overly processed. Brown sugar works too, or go sugar-free with monk fruit, erythritol, or even blended dates.
  • Eggs: Bind everything together and help the muffins rise. Room temp eggs work best for even mixing.
  • Cottage cheese: The secret weapon for soft, protein-packed muffins. Blend it first for the smoothest results.
  • Coconut oil: Keeps the muffins moist and rich. Melted butter, avocado oil, or light olive oil are all great swaps.
  • Honey or maple syrup: Adds moisture and natural sweetness. Either one works—use your fave or what’s in the pantry.
  • Baking powder: To give your muffins that bakery-style lift.
  • Baking soda: Helps with rise. 
  • Salt: Balances out the sweetness and brings out the chocolate flavor. Don’t skip it!
  • Chocolate chips: Brings the double chocolate energy. Dark, semi-sweet, or even sugar-free chips all work here.
  • Milk: Adds moisture and helps the batter come together. Use any milk you like—dairy or non-dairy both work great.

chocolate cottage cheese muffin ingredients

How To Make Chocolate Cottage Cheese Muffins

  • Preheat your oven to 350°F (180°C) and line a muffin tin with paper liners or give it a quick grease so nothing sticks.
  • Pop the cottage cheese into a blender or food processor and blitz until smooth and creamy. This step is key—it gives you that soft, even muffin crumb without any curds.

blended cottage cheese for chocolate muffins

  • In a large mixing bowl, whisk together the blended cottage cheese, eggs, coconut sugar, honey (or maple syrup), and oil until the mixture is smooth and well combined.

chocolate cottage cheese muffin mixture

  • Now add your dry ingredients: flour, protein powder, baking powder, baking soda, and salt. Gently fold everything together with a spatula until just combined. Try not to overmix—this is muffin batter, not bread dough.
  • Stir in the milk until it’s fully incorporated and the batter looks thick and chocolatey.

chocolate protein muffin mixture

  • Fold in those chocolate chips, saving a few to sprinkle on top for bakery-style flair.
  • Divide the batter between the muffin cups, filling each one right up to the top. Sprinkle those extra chocolate chips on if you’re feeling fancy.

chocolate protein muffins in tray

  • Bake for around 30 minutes, or until a toothpick poked into the center comes out clean or with just a few moist crumbs (not wet batter!).
  • Let the muffins cool on a wire rack before digging in. 

upclose chocolate muffins

Storage

Keep your muffins in an airtight container at room temperature for 2 to 3 days, or refrigerate for up to 5 days. They also freeze well so they’re a great choice for meal prepping healthy snacks in advance! 

chocolate protein muffins

Recipe Notes

  • Blend the cottage cheese: Blending it first makes the muffins extra soft and smooth—no cheese curds in sight. It also helps mellow out the tangy flavor, so you’re left with just chocolatey goodness.

  • Swap in mashed banana: Want a more naturally sweet muffin? You can sub in mashed banana for some of the coconut sugar or honey. It adds sweetness and makes the muffins extra moist.

  • Don’t overmix: Once you add the dry ingredients, stir gently and stop as soon as everything looks combined. Overmixing = dense, rubbery muffins, and nobody wants that.

  • Mix up the mix-ins: Feel free to get creative—add chopped walnuts or pecans for crunch, shredded coconut for chew, or cacao nibs if you’re a fan of deep chocolate flavor without extra sugar.

  • Warm them up: A quick 10-15 seconds in the microwave softens the muffin and melts the chocolate just enough to make it feel like it came straight from the oven. Highly recommend.

stacked chocolate protein cottage cheese muffins

Double Chocolate Chip Cottage Cheese Muffins

These bakery-style muffins are rich, chocolatey, and sneakily packed with protein—thanks to cottage cheese and a scoop of protein powder. They’re soft, moist, and just sweet enough for breakfast, snacking, or dessert.
Prep Time10 minutes
Cook Time25 minutes
Cooling Time10 minutes
Total Time45 minutes
Course: Dessert, Snack
Servings: 12 muffins
Calories: 250kcal

Ingredients

  • 1 1/2 cups all-purpose flour
  • 1 scoop chocolate protein powder
  • 1/2 cup coconut sugar
  • 2 eggs
  • 1 cup cottage cheese
  • 1/3 cup coconut oil or any oil of your choice
  • 1/3 cup honey or maple syrup
  • 1 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1/2 cup chocolate chips
  • 1/2 cup milk

Instructions

  • Preheat your oven to 350°F (180°C) and line a muffin tin with paper liners or give it a quick grease so nothing sticks.
  • Pop the cottage cheese into a blender or food processor and blitz until smooth and creamy. This step is key—it gives you that soft, even muffin crumb without any curds.
  • In a large mixing bowl, whisk together the blended cottage cheese, eggs, coconut sugar, honey (or maple syrup), and oil until the mixture is smooth and well combined.
  • Now add your dry ingredients: flour, protein powder, baking powder, baking soda, and salt. Gently fold everything together with a spatula until just combined. Try not to overmix—this is muffin batter, not bread dough.
  • Stir in the milk until it’s fully incorporated and the batter looks thick and chocolatey.
  • Fold in those chocolate chips, saving a few to sprinkle on top for bakery-style flair.
  • Divide the batter between the muffin cups, filling each one right up to the top. Sprinkle those extra chocolate chips on if you’re feeling fancy.
  • Bake for around 30 minutes, or until a toothpick poked into the center comes out clean or with just a few moist crumbs (not wet batter!).
  • Let the muffins cool on a wire rack before digging in.

Nutrition

Calories: 250kcal | Carbohydrates: 36g | Protein: 8g | Fat: 10g

If you give these double chocolate cottage cheese muffins a try, I’d love it if you could leave a star rating and a quick comment below. It helps other readers know what to expect—and it totally makes my day to hear how a recipe turned out for you. Happy baking!