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Home | Breakfast | Double Chocolate Chip Greek Yogurt Protein Muffins

Double Chocolate Chip Greek Yogurt Protein Muffins

By: Erin Indahl-Fink
Modified: February 19, 2026 - Published: January 17, 2022 - 32 Comments

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Looking for a great chocolate protein muffins recipe? These sugar free chocolate muffins are the perfect way to enjoy chocolate for breakfast without the guilt. These chocolate chip Greek yogurt muffins have 12g of protein per muffin, are made with simple ingredients, and contain NO refined sugar.

Healthy, easy chocolate muffin being held in hand, half of muffin.

Do you love bakery and coffee shop double chocolate muffins but not all the sugar and calories? For example, a triple chocolate muffin from Dunkin Donuts has 570 calories, 40 g of sugar and 29 g of fat? Most bakery, cafe and grocery store muffins are considered junk food, as they have little nutritional value, contain high amounts of sugar, unhealthy oils and excessive amounts of calories.

Making your own healthy chocolate muffins is definitely the way to go. Not only will it help you save calories in the short term, you’re saving money and making a much healthier choice with this easy chocolate muffins recipe.

Made with Greek yogurt, protein powder, eggs and other wholesome ingredients, these chocolate protein muffins are a much healthier option to the bakery or café muffin.

What do I need to make Healthy Chocolate Muffins?

These chocolate muffins come together quickly and easily. Here’s a quick-reference grocery list of the ingredients you’ll need for these easy chocolate muffins:

  • Whole wheat flour
  • Chocolate protein powder – look for a good quality protein powder with minimal ingredients.
  • Baking Powder
  • Baking Soda
  • Salt
  • Eggs
  • Plain Greek Yogurt – I like Fage plain Greek yogurt
  • Unflavored Coconut Oil – Carrington Farms Unflavored Coconut Oil is great for baking!
  • Granular monk fruit sweetener – I like Lakanto or Whole Earth granular monk fruit sweeteners
  • Vanilla extract
  • No Sugar Added Dark or Semi-Sweet Chocolate Chips – I like Lily’s brand

Are you shopping for ingredients at Target? While you’re there, pick up some of my 30 Best Healthy Target Snacks for some quick and easy healthy snack options.

Dry ingredients for healthy chocolate muffins.
Wet ingredients for easy chocolate muffins recipe.

How do I make chocolate protein muffins?

Here are the easy steps to making these chocolate muffins.

  1. In a medium bowl, whisk together your dry ingredients; whole wheat flour, chocolate protein powder, cocoa powder, baking powder, baking soda and salt. Combine well, and set aside.
  2. Next, in a larger bowl, combine your wet ingredients; plain Greek yogurt, unflavored coconut oil, granular monk fruit sweetener, eggs and vanilla extract.
Dry ingredients in bowl, and wet ingredients for healthy chocolate muffins.
Double chocolate muffin batter mixed together in clear mixing bowl.
  1. Once you’ve combined the wet and dry ingredients separately, gradually add the dry ingredients to the wet ingredients. First you can use a whisk, but the batter will become very thick, almost like brownie batter. You will then need to combine the last of the dry ingredients with a rubber scraper or wooden spoon.
  2. Lastly, stir in the chocolate chips. Fold these in and try not to overmix the batter. This can result in dry muffins.
Double chocolate muffin batter in muffin tin, topped with chocolate chips, unbaked.
Baked double chocolate muffins in muffin tin.
  1. Line a muffin tin with paper liners or silione baking cups. Spoon in the batter to each cup. Each muffin cup will be filled almost full with batter.
  2. Bake the muffins at 400 degrees for 18 minutes. To test for doneness, insert a toothpick into the center of a muffin. If the toothpick comes out clean and crumb-free the muffins are done.

Ingredient substitutions and recommendations:

  • Flour – I chose to use whole wheat flour as it has slightly more protein per ounce then all purpose. You could also use oat flour or regular all-purpose flour.
  • Chocolate chips – I chose to use Lily’s Dark Chocolate baking chips, which baked well. I also tested this recipe with a combination of half white chocolate chips and half dark, and the white chocolate chips over-browned and didn’t hold their shape. I wouldn’t recommend using white chocolate chips.
  • Protein powder – I used Orgain Organic Protein Powder, creamy chocolate fudge flavor. Use a good quality chocolate protein powder that has minimal ingredients.

Love chocolate snacks? Give my No Bake Granola Bars, Cottage Cheese Chocolate Mousse and Chocolate Protein Pudding a try! My Chocolate Protein Mug Cake, Banana Brownies, and Almond Flour Protein Balls are a fantastic snack that will satisfy your sweet tooth without the extra sugar and calories.

Stack of 3 double chocolate muffins, garnished with chocolate chips.

FAQ’s all about healthy chocolate muffins:

Why are my muffins dry?

You’ve either baked them too long, overmixed the batter or used butter instead of oil.

What is the secret to making moist muffins?

Three tips to making moist muffins: 1) Use unflavored coconut oil instead of butter; 2) Don’t over-mix the batter, and just fold in the blueberries; 3) Don’t over-bake. 18-20 minutes is ideal for the standard sized muffin.

How much sugar is in a chocolate muffin?

A Dunkin Donuts triple chocolate muffin contains 40 grams of added sugar and Au Bon Pain double chocolate muffin has 41 grams of added sugar. For a healthy chocolate muffin without refined sugar, it’s best to bake your own.

How many calories are in a double chocolate muffin from Safeway?

A Safeway bakery double chocolate muffin contains 660 calories and 37 grams of fat.

Are chocolate muffins good for you?

No, most store-bought, bakery, and café chocolate muffins are loaded with calories, refined sugar and unhealthy oils. If you enjoy chocolate muffins, it is best to bake healthy chocolate muffins at home.

Inspired to make healthier choices at breakfast? Check out some of my other recipes and resources:

  • Blueberry Cottage Cheese Muffins
  • Banana Protein Muffins
  • Breakfast Meal Prep
  • Banana Blueberry Oatmeal Muffins
  • Healthy Peach Muffins
  • Coypcat Starbucks Lemon Loaf
  • Healthy Pumpkin Muffin Recipe
  • Chocolate Avocado Smoothie
  • Chocolate Coconut Date Balls
  • Healthy Chocolate Banana Bread
  • Chocolate Protein Overnight Oats
  • Almond Joy Oatmeal Breakfast Bars
  • Lemon Poppy Seed Muffins
  • Healthy Chocolate Zucchini Muffins
  • Banana Bread with Chocolate Chunks

If you loved this Easy Chocolate Muffins recipe, check out these other ideas:

Healthy blueberry muffin sitting on top of fresh blueberries, with muffins in tin in the background.
Healthy Blueberry Muffins Recipe
Carrot cake muffins recipe topped with walnuts and cream cheese frosting.
Healthy Carrot Cake Muffins
The perfect protein muffin recipe! These Blueberry Protein Muffins are a fantastic make-ahead breakfast option for busy mornings when you want a healthy breakfast.
Blueberry Protein Muffins
These Healthy Apple Muffins will be your new favorite make-ahead breakfast. This flourless protein muffin recipe is simple to make and perfect for when you need something healthy on-the-go!
Healthy Apple Cinnamon Muffins
These Peanut Butter Banana Muffins have no flour, no oil and no refined sugar, making them the ultimate healthy snack. These flourless banana muffins come together quickly in the blender for a silky, souffle like consistency that's amazing!
Peanut Butter Banana Muffins
The perfect healthy muffin recipe that happens to taste amazing! These delicious Pumpkin Chocolate Chip Protein Muffins are loaded with protein and fiber, making them a great choice as a quick breakfast or healthy snack.
Pumpkin Chocolate Chip Protein Muffins

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Double Chocolate Chip Greek Yogurt Protein Muffins

Erin Indahl-Fink
These healthy chocolate muffins are a great option to over-sugared bakery and coffee shop muffins. Made with extra protein and NO refined sugar, these easy double chocolate muffins are a great way to enjoy chocolate for breakfast without the guilt.
No ratings yet
Healthy chocolate muffins garnished with chocolate chips and blue napkin.
Print Recipe Remove Ads Pin Recipe
Prep Time 15 minutes mins
Cook Time 18 minutes mins
Total Time 33 minutes mins
Course Breakfast
Cuisine American
Servings 12 muffins
Calories 224 kcal

Equipment

  • Mixing Bowls These stainless steel mixing bowls are super useful and a great kitchen tool!
  • Rubber Scrapers These Cuisinart rubber scraper spatulas are a fantastic kitchen utensil.
  • Muffin Pan This Wilton non-stick muffin pan is great for any muffin or cupcake recipe!

Ingredients
  

Dry Ingredients:

  • 1 cup whole wheat flour
  • 1/2 cup chocolate protein powder
  • 1/2 cup unsweetened cocoa powder
  • 2 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt

Wet Ingredients:

  • 1 1/2 cups plain Greek yogurt
  • 1/2 cup unflavored coconut oil like Carrington Farms
  • 1/3 cup granular monk fruit sweetener like Lakanto or Whole Earth
  • 2 eggs
  • 1 teaspoon vanilla extract
  • 3/4 cup no sugar added chocolate chips like Lily's

Instructions
 

  • Preheat oven to 400 degrees. Line a cupcake pan or muffin tin with paper liners or silicone baking cups. Set pan aside.
  • In a medium bowl, whisk together the dry ingredients; flour, protein powder, cocoa powder, baking powder, baking soda and salt. Set aside.
  • In large mixing bowl, whisk together the wet ingredients; yogurt, eggs, oil, granular sweetener and vanilla.
  • Gradually add the dry ingredients to the wet ingredients with a rubber scraper. The batter will become very thick, almost like brownie batter. Do your best to not overmix. Once ingredients are combined, fold in the chocolate chips.
  • Spoon the batter into the prepared pan, filling each muffin cup full.
  • Bake the muffins at 400 degrees for approximately 18 minutes. To test for doneness, insert a toothpick into the center of a muffin. If it comes out clean and crumb-free, the muffins are done.
  • Remove muffins from oven and let cool for 10-15 minutes before enjoying.

Notes

Storing muffins: Muffins can stored at room temperature in an airtight container. Will last up to 5 days. Storing the muffins in the refigerator, they will last for up to 7-10 days.
Freezing Muffins: Wrap each muffin individually in press-and-seal wrap. Muffins will keep for up to 3 months frozen. To defrost, place muffin in microwave on defrost setting (low-power) for 30-45 seconds. Heat another 30 seconds until warm.

Nutrition

Serving: 1muffinCalories: 224kcalCarbohydrates: 27gProtein: 12gFat: 14gSaturated Fat: 8gPolyunsaturated Fat: 2gCholesterol: 34mgSodium: 277mgFiber: 2gSugar: 1g
Keyword chocolate protein muffins, sugar free chocolate muffins, chocolate chip greek yogurt muffins
Tried this recipe?Let us know how it was!
Healthy chocolate muffin ingredients, batter and muffins in a muffin pan.
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Comments

  1. Graham @ Glazed & Confused says

    05.01.2014 at 4:43 pm

    You can’t play with me like this! These look SO amazing.

    So much luscious chocolate!

    Reply
  2. Laura@Baking in Pyjamas says

    05.02.2014 at 7:17 am

    Visiting from The Weekend Re-Treat. These look so yummy, I love the chips poking out of the top. I also love a nice cup of coffee on a dull and dreary day and with a nice treat on the side, even better. I co-host Sweet and Savoury Sunday and would love for you to stop by and share these and other recipes with us when the party goes live on Sunday . Have a great day!

    Reply
  3. Beverly says

    05.02.2014 at 10:51 am

    Wow, these look so awesome. I could go for one right now. Chocolate, chocolate and chocolate what more can you ask for?
    Have a great weekend,
    Bev

    Reply
  4. Ashley | The Recipe Rebel says

    05.05.2014 at 9:09 pm

    We have had some pretty dreary weather here, too, lately…. but chocolate makes everything better! Love the look of these! Saw them over on Pint-Sized Baker 🙂

    Reply
    • delightful.e.made@gmail.com says

      05.05.2014 at 9:57 pm

      Thanks so much, Ashley! You’re totally right, Chocolate makes everything better! 😉 Stop by again soon – ~E

      Reply
  5. Medeja says

    05.06.2014 at 7:28 am

    Anything with chocolate I find irresistible! Especially such muffins.. 🙂

    Reply
  6. Maria says

    05.09.2014 at 10:57 pm

    Oh my goodness… how good do these look!!!!

    Reply
  7. Deb@CookingOnTheFrontBurner says

    05.10.2014 at 1:14 pm

    Thanks for sharing with us last week at Marvelous Monday – these will be part of my features tomorrow night!

    Reply
    • delightful.e.made@gmail.com says

      05.11.2014 at 11:05 am

      Awesome!! Thanks so much, Deb!

      Reply
  8. Erlene says

    05.10.2014 at 10:05 pm

    This looks delicious and I’ve been in a muffin making mood lately. Thanks for sharing. Visiting from Sat. Link Party.

    Reply
  9. Chelsea @chelseasmessyapron says

    05.12.2014 at 4:01 pm

    These sound amazing! Triple chocolate is the best!! Pinned and sharing for SNF this weekend 🙂

    Reply
  10. Linda Warren says

    05.13.2014 at 1:09 pm

    I can never resist chocolate and with 3 kinds of chocolate I can’t wait to make this. My diet doesn’t thank you but I do. Thanks for sharing on Totally Talented Tuesdays.

    Reply
  11. Shannon {Cozy Country Living} says

    05.14.2014 at 10:47 am

    Did someone say Triple Chocolate? I’m in! These muffins look great and I bet they are delicious:) Perfect on a rainy day with a cup of coffee or tea. Pinned:)

    Reply
  12. kristi@ishouldbemoppingthefloor says

    05.15.2014 at 11:29 am

    Ohhh Erin…Yummers! One of these and a giant cup of coffee=breakfast of champions! 😉

    Reply
  13. Ai Lin says

    05.16.2014 at 7:13 am

    Whoah, what great and decadent muffins Erin! I want to make these because I too want to be loved forever. Love that they are so decadent yet so simple to make. Mmm mm! Winner.

    Reply
  14. Rachel Kathyg @ onlinesisterhood says

    05.17.2014 at 9:55 am

    Looks so amazing! pinned to try soon….stopping by form showstopper sat-congratulations on your feature:) Have a great weekend.

    Reply
  15. Kathleen R. says

    07.22.2014 at 6:04 pm

    3 different kinds of chocolate?! YUM!!

    Reply
  16. Debrashoppeno5 says

    07.24.2016 at 7:49 pm

    This recipe is made up of everything I love. I can’t wait to make and eat them.

    Reply
  17. Charlotte says

    07.25.2016 at 2:51 pm

    Moistness is a big deal to me in muffins. Thanks for sharing on Family Joy Blog Link-up. Please come back and join us again!

    Reply
  18. Helen Fern says

    07.26.2016 at 9:55 am

    Breakfast! Have this with a mocha coffee drink and I’m in heaven! Thanks for sharing on the What’s for Dinner link up!

    Reply
  19. Mother of 3 says

    07.27.2016 at 8:34 am

    Yum! You had me at triple chocolate! Pinned.

    Reply
  20. Jamie says

    07.29.2016 at 1:49 pm

    These sound amazing! My husband and son will love them – pinned them to try! 🙂 Thank you for sharing with us at the #HomeMattersParty

    Reply
  21. Theresa @DearCreatives says

    07.30.2016 at 12:24 am

    Chocolate lovers muffin recipe. Thanks for sharing at the Inspiration Spotlight party. Shared

    Reply
  22. Lisa @ Fun Money Mom says

    07.30.2016 at 5:45 pm

    YUMM! These look so delicious and I’m pinning so I can make them very soon! Thanks for sharing with us at Share The Wealth Sunday. I hope we see you again tonight!

    Reply
  23. Jennifer | The Deliberate Mom says

    07.31.2016 at 8:53 pm

    The best kind of chocolate you ask? TRIPLE CHOCOLATE! Wow, this looks and sound amazing!

    Thanks for sharing (and for linking up to the #SHINEbloghop).

    Wishing you a lovely week.
    xoxo

    Reply

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