Double Chocolate Chunk Muffins with Greek Yogurt or Cottage Cheese

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Oh yes, sweet friends! These Double Chocolate Chunk Muffins are dangerously good and I cannot wait for you to try them!! We’re talking rich, fudgy, bakery-style chocolate muffins loaded with melty chocolate chunks and the most incredibly moist centers thanks to Greek yogurt or cottage cheese.

One bite and you’ll realize these are the only chocolate muffins you’ll ever need. The smell alone will have everyone in the house hovering around the oven. Are you ready?!

Double chocolate chunk muffins with melty chocolate chips on top

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Why You’ll Love These Double Chocolate Chunk Muffins

  • SO rich and chocolatey! Cocoa powder AND chocolate chunks in every single bite. This is a chocolate lover’s dream come true!
  • Incredibly moist! The Greek yogurt (or cottage cheese) keeps these muffins so soft and tender for days. They actually get better overnight!
  • Tall, bakery-style tops! That high-heat trick gives you those gorgeous domed muffin tops that look like they came straight from a bakery.
  • Two ways to make them! Use Greek yogurt for a classic soft crumb or cottage cheese for extra fudgy richness. Both are incredible!
  • One bowl, done! No mixer needed. Just whisk, fold, scoop, and bake. So simple!

More muffins to love: these Blueberry Cottage Cheese Muffins, these Lemon Raspberry Yogurt Muffins, and these Raspberry Coffee Cake Muffins! Can we ever have enough muffin recipes?!

Bakery style double chocolate chunk muffins on cooling rack

Why Greek Yogurt and Cottage Cheese Make the Most Moist Chocolate Muffins!

So which base do you choose? Both are amazing!

  • Chocolate Greek yogurt muffins have a soft, moist crumb with classic chocolate flavor. This is the easier route since you just measure and go.
  • Chocolate cottage cheese muffins are ultra-moist with a slightly denser, richer texture and deeper chocolate flavor. Just blend the cottage cheese until completely smooth first!

I love both versions honestly. If you want that classic muffin texture, go yogurt. If you want extra moist and fudgy, go cottage cheese. You really can’t go wrong here. 🙂

Ingredients for Double Chocolate Chunk Muffins

Let’s talk about what you need for these chocolate chunk beauties!

Wet Ingredients for Chocolate Chunk Muffins

  • 2 large eggs
  • 1 cup granulated sugar
  • 1/2 cup neutral oil (or melted butter for even richer flavor)
  • 1 cup Greek yogurt or blended cottage cheese
  • 2 teaspoons vanilla extract
  • 1/2 cup hot coffee or hot water (this blooms the cocoa and makes the chocolate flavor so much deeper!)

Dry Ingredients for Chocolate Muffins

  • 1 3/4 cups all-purpose flour
  • 1/2 cup unsweetened cocoa powder
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon fine salt

Chocolate Chunk Mix-Ins

  • 1 cup chocolate chips or chunks
  • 1/2 cup mini chips for topping (optional but so worth it!)

Freshly baked muffins with tall domed tops in pan with cottage cheese or Greek yogurt

How to Make Double Chocolate Chunk Muffins

Prep

  1. Preheat oven to 425°F.
  2. Line a 12-cup muffin pan with paper liners.

Blend the Cottage Cheese (If Using)

  1. Blend 1 cup cottage cheese until completely smooth. No lumps! If using Greek yogurt, skip this step.

Whisk the Chocolate Muffin Batter

  1. In a large bowl, whisk together 2 eggs, 1 cup sugar, 1/2 cup oil, 1 cup yogurt or blended cottage cheese, and 2 teaspoons vanilla.
  2. Slowly pour in 1/2 cup hot coffee and whisk quickly to combine.

Add the Dry Ingredients

  1. In a separate bowl, whisk together 1 3/4 cups flour, 1/2 cup cocoa powder, 2 teaspoons baking powder, 1/2 teaspoon baking soda, and 1/2 teaspoon salt.
  2. Add the dry ingredients to the wet and fold gently until just combined. Don’t overmix this! A few streaks of flour are totally fine.
  3. Fold in 1 cup chocolate chips or chunks.

Fill and Bake Your Chocolate Chunk Muffins

  1. Divide batter evenly among the 12 muffin cups, filling each about 3/4 full. Press a few mini chips on top if you’d like!
  2. Bake at 425°F for 5 minutes, then reduce to 350°F for 13 to 15 minutes. The high heat start is the trick for those tall, dramatic muffin tops!
  3. Cool 10 minutes in the pan, then transfer to a wire rack.

Rich dark batter with cocoa powder in mixing bowl

Tips for the Best Bakery Style Protein Chocolate Muffins

  • Don’t skip the hot coffee! I’m telling you right now, this is the trick that takes these from good to incredible. It makes the chocolate flavor SO much richer and deeper. Hot water works too if you don’t have coffee on hand.
  • Don’t overmix the batter. Fold the dry ingredients in gently until just combined. Overmixed muffins turn out tough and dense. Nobody wants that!
  • Use quality cocoa powder. Dutch-process cocoa gives a darker, richer flavor. Natural cocoa works great too but the flavor will be slightly lighter.
  • The 425 to 350 bake is everything. That blast of high heat at the start is what gives you those tall, gorgeous bakery-style domes. Don’t skip this step, I promise it matters!
  • Fill cups 3/4 full. If you fill them all the way to the top, they’ll overflow and you’ll have a mess. Trust me on this one. 🙂

Moist chocolate muffin split open showing fudgy interior with cottage cheese or Greek yogurt

How to Store Chocolate Chunk Muffins

  • Store muffins in an airtight container at room temperature for up to 3 days. They actually taste even better the next day because the flavors develop overnight!
  • For longer storage, freeze muffins in a zip-top bag for up to 2 months. Thaw at room temperature or pop one in the microwave for 20 to 30 seconds. Future you will be so happy!

More Double Chocolate Chunk Muffin Variations

  • Peanut butter swirl: Drop a teaspoon of peanut butter on top of each muffin before baking and swirl with a toothpick. So good!
  • Mint chocolate: Add 1/2 teaspoon peppermint extract and fold in chopped Andes mints instead of chocolate chips.
  • Mocha muffins: Add 1 tablespoon instant espresso powder to the dry ingredients for an extra coffee kick.
  • White chocolate chunk: Swap half the dark chocolate chunks for white chocolate chips. That contrast is everything!
  • Mexican chocolate: Add 1/2 teaspoon cinnamon and a tiny pinch of cayenne to the dry ingredients for a warm, spicy twist.

Love baking with cottage cheese? Check out this Cottage Cheese Banana Bread and this Double Chocolate Banana Bread! Plus, grab the 20 Dessert Recipes Using Greek Yogurt Cookbook for even more yogurt-based baking inspiration!

Double Chocolate Chunk Muffin FAQs

Can I use regular yogurt instead of Greek yogurt in chocolate muffins?

Yes, but Greek yogurt works best because it’s thicker and adds more moisture. If using regular yogurt, use 3/4 cup instead of 1 cup since it has more liquid. The muffins will still be delicious but slightly less dense and rich.

Why did my muffins sink in the middle?

The most common reason is overmixing the batter or opening the oven door too early. Mix until just combined and resist peeking for at least the first 15 minutes of baking. Also make sure your baking powder is fresh! Old leavening agents lose their lift.

Can I make these muffins ahead of time?

These muffins are great for meal prep! Bake a batch, cool completely, and store in an airtight container. They’ll stay fresh at room temperature for 3 days or in the freezer for up to 2 months. Just grab one and go!

Do these chocolate cottage cheese muffins taste like cottage cheese?

Not at all! Once blended smooth, the cottage cheese completely disappears into the batter. All you taste is rich, deep chocolate. The cottage cheese just adds incredible moisture behind the scenes. Nobody will know it’s in there unless you tell them!

What makes these chocolate muffins so moist?

It’s all about the base! Greek yogurt and cottage cheese add tons of moisture to the batter, which keeps these muffins soft and tender for days. The hot coffee helps too by making the chocolate flavor richer and the crumb even more fudgy!

Stack of chocolate cottage cheese muffins with chocolate chunks with cottage cheese or Greek yogurt

So are you ready for the most rich, fudgy, melt-in-your-mouth, chocolate-loaded muffins with those gorgeous bakery-style tops?! These Double Chocolate Chunk Muffins are pure chocolate heaven and I just know you’re going to love them!! Time to get baking! Happy Baking!

Want more quick ideas and dessert inspo? Follow on Pinterest, Instagram and Facebook for recipe updates, baking tips, and lots of sweet inspiration.

More Yogurt & Cottage Cheese Recipes

Double Chocolate Chunk Muffins

Rich, fudgy double chocolate chunk muffins with a protein boost from Greek yogurt or cottage cheese. Bakery-style tall tops, incredibly moist centers, and loaded with melty chocolate chunks.
No ratings yet
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast, Dessert, Snack
Cuisine American
Servings 12 muffins
Calories 354 kcal

Equipment

  • 12-cup muffin pan
  • Paper muffin liners
  • Large mixing bowl
  • Whisk
  • Blender (if using cottage cheese)

Ingredients
  

Wet Ingredients

  • 2 large eggs
  • 1 cup granulated sugar
  • ½ cup neutral oil or melted butter for richer flavor
  • 1 cup Greek yogurt or blended cottage cheese see notes
  • 2 teaspoons vanilla extract
  • ½ cup hot coffee or hot water blooms the cocoa

Dry Ingredients

Mix-Ins

  • 1 cup chocolate chips or chunks
  • ½ cup mini chocolate chips for topping optional

Instructions
 

  • Preheat oven to 425°F. Line a 12-cup muffin pan with paper liners.
  • If using cottage cheese: Blend 1 cup cottage cheese until completely smooth with no lumps. If using Greek yogurt, skip this step.
  • In a large bowl, whisk together 2 eggs, 1 cup granulated sugar, 1/2 cup oil, 1 cup yogurt or blended cottage cheese, and 2 teaspoons vanilla extract.
  • Slowly pour in 1/2 cup hot coffee (or hot water) and whisk quickly to combine.
  • In a separate bowl, whisk together 1 3/4 cups flour, 1/2 cup cocoa powder, 2 teaspoons baking powder, 1/2 teaspoon baking soda, and 1/2 teaspoon salt.
  • Add the dry ingredients to the wet and fold gently until just combined. Do not overmix. A few streaks of flour are fine.
  • Fold in 1 cup chocolate chips or chunks.
  • Divide batter evenly among the 12 muffin cups, filling each about 3/4 full. Press a few mini chips on top if desired.
  • Bake at 425°F for 5 minutes, then reduce temperature to 350°F and bake for 13 to 15 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs.
  • Cool in the pan for 10 minutes, then transfer muffins to a wire rack to cool completely.

Notes

Greek yogurt vs. cottage cheese: Greek yogurt gives a soft, classic muffin crumb with moderate protein. Blended cottage cheese creates a denser, ultra-moist texture with higher protein. Both are delicious!
Hot coffee tip: The hot liquid blooms the cocoa powder and intensifies the chocolate flavor. Hot water works as a substitute.
Storage: Store in an airtight container at room temperature for up to 3 days, or freeze for up to 2 months.
Nutrition note: Values are estimates based on the Greek yogurt version. Cottage cheese version will have slightly higher protein.

Nutrition

Serving: 1gCalories: 354kcalCarbohydrates: 48gProtein: 5gFat: 17gSaturated Fat: 6gPolyunsaturated Fat: 5gMonounsaturated Fat: 3gTrans Fat: 0.1gCholesterol: 34mgSodium: 157mgPotassium: 217mgFiber: 2gSugar: 31gVitamin A: 61IUVitamin C: 0.05mgCalcium: 78mgIron: 2mg
Keyword baked, bakery style muffins, chocolate, chocolate muffins, cottage cheese muffins, double chocolate chunk muffins, muffins, protein muffins, rich, yogurt muffins
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