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Home » Recipes » Muffins

Chocolate Sourdough Protein Muffins (Healthy AND Tasty!)

by Haylee Jane Monteiro · Modified: Feb 21, 2026 · Published: Dec 29, 2025
This post may contain affiliate links.

Not-your-average Chocolate Sourdough PROTEIN Muffin that's perfectly balanced, high protein, low calorie, low fat and sugar free! It certainly proves that healthy can be delicious!

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Looking for a way to use up your sourdough discard that's both healthy and delicious? This is exactly how this recipe came to be, so say hello to these sourdough discard chocolate protein muffins! It's the ideal way to get rid of that extra starter while making a treat that feels indulgent but is secretly super good for you.

These muffins are a game-changer for a high-protein, guilt-free breakfast or snack. Packed with rich cocoa flavor and protein from the protein powder as well as Greek yogurt, this sourdough discard muffin recipe is a must-have if you're on a macro-friendly eating journey.

Ingredients for Chocolate Sourdough Protein Muffins!

The chocolate sourdough protein muffins are made with a combination of healthy and delicious ingredients.

  • Flour: The base of these muffins; I used 1:1 gluten free baking flour, but you can use all purpose or whole wheat pastry flour too
  • Chocolate Protein Powder: Adds a rich chocolate flavor, and the protein boost, but also serves as the source of sweetness! I use the chocolate whey-casein from Quest.
    Make sure you use a protein powder that is sweet enough.
    • Substitute: Try a plant-based protein if you prefer. I recommend KOS or Truvani.
    • Substitute: f you don't have chocolate, you can swap it for vanilla protein powder.
  • Unflavored Protein Powder: This adds to the protein content as a replacement for some of the flour without altering the flavor profile. The one I use is the plant-based protein from KOS.
    • Substitute: Replace this with ¼ cup extra flour.
  • Unsweetened Cocoa Powder: Enhances the chocolate taste without adding extra sugar; The sweetness comes from the protein powder.
  • Baking Powder and Baking Soda: The leavening agents that work with the sourdough starter for a good rise.
  • Unsweetened Applesauce: This adds moisture (and a bit of sweetness too) while reducing the need for added fats.
    • Substitute: Use mashed banana or pumpkin puree, but this may slightly alter the flavor and color.
  • Nonfat Plain Greek Yogurt: Also adds moisture, but also protein to the chocolate sourdough muffins.
    • Substitute: Full-fat Greek yogurt or low-fat wil also work just as well. You can also use a dairy-free thick coconut yogurt. Just be sure to use a thick yogurt.
  • Unsweetened Almond Milk: Helps to create the right consistency for the batter.
    • Substitute: Any unsweetened milk alternative (soy, oat, cashew) or even dairy milk works well.
  • Unfed Sourdough Starter: Often referred to as "sourdough discard." his is the core for the sourdough muffins; It also contributes a unique depth of flavor in these muffins.
    • Substitute: You can use fed starter, but the unfed/discard has a nice tang without compromising the structure of the muffins.
  • Vanilla Extract: People tend to skip it, but the vanilla really enhances the overall flavor with the chocolate.
  • Egg: Acts as a binder!

See recipe card at the bottom of the page for the measurements!

Not-your-average Chocolate Sourdough PROTEIN Muffin that’s perfectly balanced, high protein, low calorie, low fat and sugar free! It certainly proves that healthy can be delicious!

How to make High Protein Chocolate Muffins with Sourdough Discard

Follow these simple steps to make these perfect sourdough discard chocolate protein muffins:

  1. Preheat & Prep: Preheat your oven to 425°F (220°C) and line 10 cups of a muffin pan with cupcake liners. Just to be safe, lightly spray the insides of the liners with cooking spray.
  2. Mix Dry Ingredients: In a large bowl, whisk together the flour, chocolate protein powder, unflavored protein powder, unsweetened cocoa powder, baking powder, and baking soda.
  3. Mix Wet Ingredients: In a separate medium bowl, whisk together the unsweetened applesauce, Greek yogurt, almond milk, sourdough discard, vanilla extract, and egg until well combined and smooth.
  4. Combine Wet and Dry: Pour the wet ingredients into the bowl of dry ingredients. Use a large spoon or spatula and mix until just combined.
    Do not overmix; a few lumps are perfectly fine. Overmixing can lead to tough, dense muffins. The batter should be thick.
  5. Fill Muffin Cups: Divide the batter evenly among the 10 muffin cups, filling them about ¾ of the way to the top. If you're feeling fancy, sprinkle some sugar-free chocolate chips or other toppings on top.
  6. Start Baking: Place the muffin pan in the preheated oven and bake for the first 5 minutes at 425°F. 
  7. Finish Baking: After 5 minutes, lower the oven temperature to 350°F and continue to bake for another 13-15 minutes (for a total baking time of 18-20 minutes).
    Insert a toothpick into the center and make sure it comes out dry.
  8. Cool: Let the muffins cool in the pan for 10 minutes before transferring them to a wire rack to cool completely.

Tips to make the perfect Protein Muffins with Sourdough Starter

While this recipe is easy, there are a few things to keep in mind to makie these whey protein muffins.

  • Grease the cupcake liners with cooking spray - this will allow the muffins to come off easily!
  • Use room temperature eggs and room temperature milk.
  • Don't Overmix: Overmixing the batter can lead to tough muffins. It will activate the gluten in the flour, and together with the protein powder will make your muffins dense instead of light and fluffy.
  • Taste the batter and see if you need some extra sweetener (I'd recommend stevia if needed). You can add a little more stevia if you prefer a sweeter muffin.
  • Don't Overmix: This is the most important rule for this recipe! 
  • The Two-Temperature Bake: The initial high heat at 425°F creates that classic dome-like muffin top. Dropping the temperature allows the inside to cook through without burning the outside.

Equipment

I recommend baking these muffins in a good, non-stick muffin pan.

Storage Instructions for Macro Friendly Sourdough Chocolate Muffins

These macro friendly sourdough chocolate muffins are best enjoyed fresh but also great for meal prep. Here's what you can do to keep them longer:

Freezer: For longer storage, you can freeze the muffins for up to 3 months. Keep them in an airtight container or ziploc bag.
To defrost: Let the muffins thaw at room temperature, or warm them briefly in the microwave or oven.

Countertop: They can be stored in an airtight container at room temperature for up to 3 days

Fridge: For longer freshness, store the diet friendly sourdough chocolate muffins in the fridge for up to 5 days. You can reheat them in the microwave for a few seconds to warm them if you'd like!

Not-your-average Chocolate Sourdough PROTEIN Muffin that’s perfectly balanced, high protein, low calorie, low fat and sugar free! It certainly proves that healthy can be delicious!

FAQs

Are these muffins truly sourdough discard muffins with no sugar?

Yes! This recipe is has no added sugar, and gets its sweetness from the protein powder and a little from the unsweetened applesauce.This really is a good option for someone watching their sugar intake.

Can I use fed sourdough starter instead of discard?

I haven't tried it myself so I can't confirm how they'll turn out, but you can certainly try to make these muffins with fresh fed starter.

Can I make these muffins gluten-free?

If you have a gluten free sourdough discard and use gluten-free all-purpose flour blend in place of the regular flour, you can turn this chocolate muffin recipe gluten-free.

More Healthy Chocolate Protein Muffin:

If you were interested in this muffin recipe, here's some more recipes you might like:

  • Chocolate Banana Protein Muffins in a Blender
  • Low Calorie Chocolate Protein Muffins - Moist, but Oil Free
  • Single Serve Chocolate Protein Muffin (but so big!)
  • Chocolate Pumpkin Protein Muffins - Amazing and Healthy!

Did you try this recipe? I'd LOVE to know!
 Tag @hayls.kitchen on Instagram & leave a ⭐️⭐️⭐️⭐️⭐️ review below!

Not-your-average Chocolate Sourdough PROTEIN Muffin that's perfectly balanced, high protein, low calorie, low fat and sugar free! It certainly proves that healthy can be delicious!

Chocolate Sourdough Protein Muffins (Healthy AND Tasty!)

5 from 2 votes
Print recipe Pin Recipe
Prep Time15 minutes mins
Cook Time20 minutes mins
Total Time35 minutes mins
Servings: 10 muffins
Calories: 95kcal
Course: Breakfast
Cuisine: American
Not-your-average Chocolate Sourdough PROTEIN Muffin that's perfectly balanced, high protein, low calorie, low fat and sugar free! It certainly proves that healthy can be delicious!

Ingredients

  • 100 g Flour
  • ½ cup Chocolate Protein Powder, Whey-Casein, 45g
  • 3 tablespoon Unflavored Protein Powder, Plant-based, 17g
  • ¼ cup Unsweetened Cocoa Powde, 20g
  • 1 teaspoon Baking Powder
  • ¼ teaspoon Baking Soda
  • 100 g Unsweetened Applesauce
  • ½ cup Nonfat Plain Greek Yogurt, 112g
  • ¼ cup Unsweetened Almond Milk, 60ml
  • ¼ cup Unfed Sourdough Starter (Sourdough Discard), 62g
  • 1 teaspoon Vanilla Extract
  • 1 Egg
Are you Making This?

Please leave a ⭐⭐⭐⭐⭐ comment below letting me know what you think! This supports my page so I can continue to give you free recipes. Even 1 sentence is enough 🙂

Instructions

  • Preheat oven to 425°F, line 10 cups of a muffin pan with cupcake liners, and lightly spray insides with cooking spray (or use non-stick pan).
  • In a large bowl, whisk together the flour, chocolate protein powder, unsweetened cocoa powder, unflavored protein powder, baking powder, and baking soda.
  • In a separate medium bowl, whisk together the unsweetened applesauce, nonfat plain Greek yogurt, unsweetened almond milk, unfed sourdough starter, vanilla extract, and egg until well combined.
  • Pour the wet ingredients into the dry ingredients. Mix with a spoon or spatula until just combined. Be careful not to overmix; a few lumps are okay. You should have a thick muffin batter.
  • Divide the batter among muffin cups, about ¾ way to the top. Sprinkle chocolate chips or other toppings if needed.
  • Bake the first 5 minutes at 425°F in the preheated oven. Lower the oven temperature to 350°F and continue to bake the muffins for another 13-15 minutes (13-20 minutes in total). A toothpick inserted into the center comes out dry.
  • Cool for 10 minutes, then remove pan. Transfer to a wire rack to cool completely, about 15 minutes, and enjoy.

Video

Notes

  • Taste the batter and see if you need some extra sweetener; I'd recommend stevia if needed.
  • Nutrition value is calculated using products recommended below and includes chocolate chips.
Product Recommendations:
  • Quest Nutrition Chocolate Whey-Casein Protein Powder
  • KOS Plant Unflavored Protein Powder
  •  
Nutrition:
  • Servings: 10 muffins | Serving size: 1
  • Calories: 95 cal
  • Fat: 1.2g | Saturated fat: 0.4g
  • Carbohydrates: 14.1g | Fiber: 1.8g | Sugar: 1.4g
  • Protein: 7.6g
Posting your remake? Tag me on IG @hayls.kitchen!

More Recipes You'll Love

  • Banana Protein Muffins Without Protein Powder - Easy Blender Recipe
  • Protein Cornbread Muffins - Sweet, Savory and Beautiful
  • Single Serve Blueberry Protein Muffin - Big and Beautiful!
  • Gingerbread Protein Muffins - Easy, Festive, Healthy!

Comments

  1. Nicole says

    August 09, 2026 at 4:25 am

    5 stars
    These muffins are moist and delicious! It’s so kind of you to share your talents. Thank you so much for a baked good that will sustain me and tastes great!

    Reply
    • Haylee Jane Monteiro says

      August 30, 2026 at 11:01 am

      I'm so so glad to hear that you liked these sourdough muffins Nicole <3 It genuinely means so much.
      And I would actually love to hear back on any other recipes you try!

      Reply
  2. Roberta says

    June 04, 2026 at 8:38 am

    5 stars
    so excited to try this! we love sourdough, as a mom I'm excited to sneak more protein into kids diet. But I need to express my ultimate amazement at your recipe being by weight. The kids help with baking, baking by weight limits dishes soooo much!! And very few recipes I find for us to try are actually done by weight. Also weight recipes turn out more consistent results vs cups recipes, especially when the littles are the ones measuring

    Reply
    • Haylee Jane Monteiro says

      July 10, 2026 at 11:07 pm

      This comment absolutely made my day! As someone who tracks macros herself and is a Type A person I'm all about precision, so baking by weight is my favorite way to guarantee perfect results. Plus, avoiding a mountain of dirty dishes is a massive win when baking with little helpers! I hope you and the kids have so much fun making these together and love every bite 🙂

      Reply

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Hi, I'm Haylee!

I use my passion for baking (and my sweet tooth) to create healthy, high protein, low fat and sugar free desserts and sweet treats that are actually delicious.

Come join me in Hayl's Kitchen and let's eat high protein, sweet and guilt free!

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