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A close-up of freshly baked blueberry protein muffins, made with sourdough discard, sitting in a muffin tin. One muffin is torn in half, revealing a soft, fluffy interior packed with blueberries.
Sourdough Discard Muffins

Low-Sugar Blueberry Protein Muffins with Sourdough Discard

Moist, rich, and bursting with flavor—the perfect baking recipe for blueberry season. Enjoy these blueberry protein muffins for breakfast, a snack, or dessert.

Prep: 10 minutes
Cook: 30 minutes
Total: 40 minutes
Jump to Recipe Rate Recipe
Recipe Index | Ferment | Sourdough Discard | Sourdough Discard Muffins

Low-Sugar Blueberry Protein Muffins with Sourdough Discard

Moist, rich, and bursting with flavor—the perfect baking recipe for blueberry season. Enjoy these blueberry protein muffins for breakfast, a snack, or dessert.

A close-up of freshly baked blueberry protein muffins, made with sourdough discard, sitting in a muffin tin. One muffin is torn in half, revealing a soft, fluffy interior packed with blueberries.

Low-sugar Blueberry Protein Muffins

If you love baking with sourdough starter and are looking for a creative way to use your sourdough starter discard, we have a delightful treat for you: Blueberry Protein Muffins with Sourdough Discard!

These muffins include fresh, juicy blueberries and organic whey protein powder for delectably nutritious muffins.

A close-up of freshly baked blueberry protein muffins, made with sourdough discard, sitting in a muffin tin. One muffin is torn in half, revealing a soft, fluffy interior packed with blueberries.

Blueberry Protein Muffins with Sourdough Discard

The fermentation process used to create sourdough bread enhances its nutritional profile. Sourdough is easier to digest than traditional yeast bread. In sourdough, lactic acid bacteria break down gluten, fructans, and phytic acid. This can be particularly beneficial for individuals with gluten or FODMAP sensitivities.

Muffins are not usually long-fermented, but they can be! I don’t long ferment these blueberry sourdough muffins, but many readers have told me they have successfully fermented the batter overnight in the fridge for easier digestion. You can try fermenting the muffin batter overnight in the fridge before preheating your oven and filling your muffin tin with batter.

Don’t Over-Mix These Blueberry Protein Muffins

One crucial tip when making these blueberry protein muffins is to avoid overmixing the batter. Overmixing can result in dense muffins rather than light and fluffy protein muffins, and the reason behind this is the formation of gluten.

Gluten, a protein present in flour, gives structure to baked goods. However, excessive mixing develops gluten strands, leading to a denser texture. To prevent this, gently mix the dry and wet ingredients until they are just combined, ensuring there are still some lumps and streaks of flour in the batter.

This technique allows the muffins to rise correctly, resulting in a tender crumb.

My other muffin baking tip is always to use a thin metal aluminum muffin tin with paper liners. A metal muffin tin works way better than a silicone muffin pan.

Why Are My Protein Muffins Dry?

Dry protein muffins can result from several factors related to ingredients and baking techniques. Here are some common reasons and tips to help you troubleshoot:

  1. Too Much Flour: Adding too much flour can make muffins dry. For accuracy, measure your flour correctly using the spoon-and-level method or a kitchen scale.
  2. Overmixing: Overmixing the batter can cause too much gluten to develop, making the muffins dense and dry. Mix until just combined to avoid this.
  3. Baking Time: Baking muffins for too long can cause them to dry out. Check them a few minutes before the recipe’s suggested time by inserting a toothpick; it should come out clean but not dry.
  4. Protein Powder Type: Different protein powders absorb moisture differently. Whey protein, for example, can sometimes make baked goods dry. The blueberries used in this recipe add enough moisture to keep the muffins moist, even with protein powder.
  5. Low-Fat Content: If your recipe uses low-fat ingredients or substitutes, the muffins may lack moisture. My recipe calls for grass-fed butter, which helps keep the muffins from drying out.

What is the Secret to Moist Muffins?

Adding fruit into muffins is the secret to achieving a moist and tender texture that keeps these baked treats irresistibly soft.

Fruits like blueberries, apples, and cherries naturally contain high water content, which releases moisture as the muffins bake. This moisture infusion prevents the muffins from drying out and enhances their softness. Moreover, fruits contribute to the flavor profile, adding a fresh, natural sweetness that complements the other ingredients.

The natural sugars in blueberries also caramelize during baking, creating pockets of juicy, flavorful bites within the muffin. The pectin found in fruits is a natural thickener, contributing to the moist, luscious crumb. Incorporating fruit elevates the taste and ensures that each muffin is tender and deliciously moist.

A freshly baked blueberry protein muffin, made with sourdough discard, is torn in half on crinkled parchment paper, revealing a moist, fluffy crumb filled with juicy blueberries.

Storing Blueberry Protein Muffins

Storing baked blueberry protein muffins properly ensures they remain fresh and delicious. Here are some tips on how to store them effectively:

  • Room Temperature Storage:
    • Allow muffins to cool completely.
    • Place them in an airtight container lined with paper towels to absorb excess moisture.
    • Store at room temperature for up to 3-4 days.
  • Refrigeration:
    • If the weather is hot or humid, consider refrigerating muffins.
    • Store in an airtight container in the fridge for up to one week.
  • Freezing Muffins:
    • Cool muffins completely before freezing.
    • Place muffins in a freezer-safe bag or container.
    • Label it with the date and freeze it for up to 3 months.
  • Reheating Frozen Muffins:
    • Remove the desired number of muffins from the freezer.
    • Microwave on high for 20-30 seconds or until warm.
    • Alternatively, preheat the oven to 350°F (175°C) and heat muffins for 10-15 minutes until warmed.

More Sourdough Discard Muffin Recipes

  • Zucchini Blueberry Muffins with Sourdough Discard
  • Double Chocolate Cherry Muffins with Sourdough Discard
  • Oatmeal Chocolate Chip Muffins with Sourdough Discard
A close-up of freshly baked blueberry protein muffins, made with sourdough discard, sitting in a muffin tin. One muffin is torn in half, revealing a soft, fluffy interior packed with blueberries.

Things You May Need:

12-Well Muffin Pan

12-Well Muffin Pan

A product image of a counter top oven showing the front face

Breville Smart Oven Air Fryer Pro

Bone Broth Protein Powder

Bone Broth Protein Powder

Handmade Mixing Bowls

Handmade Mixing Bowls

three sourdough spurtles made of wood

Teakwood Stirring Spatula for Sourdough

Print
A close-up of freshly baked blueberry protein muffins, made with sourdough discard, sitting in a muffin tin. One muffin is torn in half, revealing a soft, fluffy interior packed with blueberries.
Sourdough Discard Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

4.9 from 12 reviews

Low-Sugar Blueberry Protein Muffins with Sourdough Discard

A high-protein sweet snack that uses up some sourdough discard? Sign us up! Moist, rich, and bursting with flavor—the perfect baking recipe for blueberry season. Enjoy these blueberry protein muffins for breakfast, a snack, or dessert.

  • Prep: 10 minutes
  • Cook: 30 minutes
  • Total Time: 40 minutes

Ingredients

  • 1 3/4 cups all-purpose flour
  • 3/4 cup plain whey protein powder
  • 1/2 cup brown sugar, packed
  • 1/2 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1 teaspoon salt
  • 2 cups fresh blueberries, slightly mashed
  • 1/2 cup grass-fed butter, room temperature soft
  • 1/2 cup sourdough starter, room temperature
  • 2 teaspoons vanilla extract
  • 1/3 cup whole milk, room temperature
  • 2 eggs, room temperature

Instructions

  1. Preheat your oven to 350° F.
  2. Line a muffin tin with paper liners.
  3. lightly mash the blueberries with fork.
  4. In a medium-large mixing bowl, combine the flour, protein powder, brown sugar, baking soda, baking powder, salt, and blueberries.
  5. In a separate bowl, combine the butter, sourdough starter, vanilla, whole milk, and two eggs. Whisk until combined.
  6. Gently fold the wet ingredients into the dry ingredients until everything is just combined. Do not over-mix. The batter should be thick, and it’s okay if there are clumps.
  7. Spoon the batter into the muffin tins. Optional— top with extra blueberries
  8. Bake for about 30 minutes total. Rotate the pan halfway through.
  9. Allow cooling for about 15 minutes.

Notes

  • If you do not have protein powder, you can still make these muffins!— Use 2 cups of flour total in the recipe, and omit the protein powder.

Did you make this recipe?

Please leave a 5-star review below if you loved it! Tag @cultured.guru on Instagram

 

Nutrition information is auto-calculated and estimated as close as possible. We are not responsible for any errors. We have tested the recipe for accuracy, but your results may vary.

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Kaitlynn Fenley Author, Educator, Food Microbiologist
Kaitlynn is a food microbiologist and fermentation expert teaching people how to ferment foods and drinks at home.
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hey i’m kaitlynn, i’m a microbiologist and together with my husband jon we are cultured guru.

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  1. Amy
    08|31|2024

    These were delicious! I added juice of 1 lemon + zest to add some zing to it.

    Reply
    1. Kaitlynn Fenley
      09|03|2024

      love that! Blueberry and lemon are fantastic together!

      Reply
  2. Monica
    10|15|2024

    These turned out fantastic!!! My one year old loves them too! They are perfect- crispy on the outside but light and soft on the inside. New favorite blueberry muffin recipe!

    Reply
  3. Julia
    01|12|2025

    Delicious! These muffins have a wonderful crunchy top and are soft and fluffy inside. I fermented the batter overnight in the fridge and they baked great. I also used frozen blueberries from last years’ harvest (just let blueberries thaw at room temp and don’t include excess liquid).

    Reply
    1. Kaitlynn Fenley
      01|13|2025

      Thanks for leaving a review! I’m glad to hear the overnight batter ferment worked great for you too!

      Reply
      1. Julia
        01|29|2025

        I made these again, but used bananas instead of blueberries and 1/2 whole wheat flour. Still delicious!

        Reply
  4. Brittany
    01|15|2025

    I used vanilla protein powder and only 1 teaspoon vanilla extract to its not too vanillily. Came out perfect 👌 they were so moist and I dint feel bad about eating them. I baked a handful for the kids breakfast to grab and go!

    Reply
    1. Kaitlynn Fenley
      01|16|2025

      Thank you so much for leaving a review and for trying my recipe!

      Reply
  5. Morgan
    01|20|2025

    These turned out so great! Loved how they were crispy on the stop but still soft and chewy on the inside. I also used a plant based protein powder and fermented them overnight and they still turned out great

    Reply
    1. Kaitlynn Fenley
      01|20|2025

      Thank you for leaving a review! I’m thrilled to hear you loved the recipe.

      Reply
  6. Sabre
    01|27|2025

    Easy recipe. I use about 1/2 cup pea protein 1/4 cup collagen powder. Leave out some of the flour and add hemp and flax seeds. I used thawed frozen blueberries. Added a ripe mashed banana to the wet ingredients. Also added about 1/2 cup cottage cheese. Dash of cinnamon. Let ferment in the fridge 8-10 hours. Better rise if the batter comes to room temp before baking. Works well for mini muffins too baked for about 15 min.

    Reply
  7. Anonymous
    01|28|2025

    this is under sourdough discard, but the recipe calls for sourdough starter…so does it have to be active sourdough starter or can it be discard i have in the fridge? can you make these without the protein powder?

    Reply
    1. Kaitlynn Fenley
      01|28|2025

      You can use active starter or discard from your fridge. Both work. Either way the starter is “discarded” into the recipe because it is not used for rise. You can uses 2 cups flour total and leave out the protein powder.

      Reply
  8. Anonymous
    01|29|2025

    They turned out great. It made 18 muffins so I’m not sure what went wrong, but I’m not mad.

    Reply
    1. Kaitlynn Fenley
      01|30|2025

      hmm… maybe your muffin tin is a different size than mine!

      Reply
  9. Saskia
    03|08|2025

    We love these! I feed my starter weekly and make these atleast every other week. They really are delish.

    Reply
    1. Kaitlynn Fenley
      03|13|2025

      Glad to hear y’all are loving the muffins! Thanks for leaving a review!

      Reply
  10. Parker
    04|10|2025

    Made these last week, and they were so good!! For my next batch, I wanted to try with chocolate chips – do you think this will significantly affect how moist they are?

    Reply
    1. Kaitlynn Fenley
      04|11|2025

      yes! Without the blueberries they will be quite dry. If you want to do chocolate chips, sub the blueberries for some chopped banana maybe? Fresh fruit is necessary.

      Reply
  11. Katherine
    05|20|2025

    Could I add a couple extra egg whites to up the protein? Would that make the batter too runny?

    Reply
    1. Kaitlynn Fenley
      05|20|2025

      It will definitely make the batter wetter, which will change the final texture. I’d say just adjust the egg. You can do 4 servings of egg white instead of two eggs. I haven’t tested the recipe like that though, so I cant know for sure how that will come out.

      Reply
  12. Madison
    05|28|2025

    The brown sugar wasn’t included in the directions so I forgot to add until the end but they still turned out delicious!

    Reply
    1. Kaitlynn Fenley
      05|28|2025

      oh! I see, I have “sugar” in the directions not “brown sugar”

      I just updated it to be more exact! Thanks for the feedback.

      Reply
  13. Joe
    07|20|2025

    I like these as a light breakfast. An easy recipe to follow, nice reults each time I’ve made them.

    Reply
  14. Wendy Walker
    08|23|2025

    Love these!!!

    Reply
  15. Rachel
    10|01|2025

    I want to try replacing the brown sugar with honey (The recipe is amazing as written, I just always have honey on hand but I don’t always have brown sugar). Any thoughts on how to adjust things?

    Reply
    1. Kaitlynn Fenley
      10|02|2025

      I’m not too sure, and I’d need to test it to know since you’d be subbing a dry ingredient for a wet ingredient!

      Reply

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My favorite topic I teach in our online course is My favorite topic I teach in our online course is called Fermentation Variables. The whole lesson is centered around the fact that there are six main variables that influence the outcome of fermentation.

Here they are, in no particular order:

Sugar
Salt
Oxygen
Acidity
Temperature
Time

Temperature and time depend on each other most closely. 

that means, for all of our foods and drinks that ferment at room temp, things slow way down in the winter cold. 

The fermentation timeline is simply longer when it’s colder (and faster when it’s hotter). The microbes, kind of like us, make things happen slowly in the cold winter. 

I think this is yet another sign from nature that we’re supposed to rest and be gentle and gracious with deadlines, work, and not rush things this time of year. 

Let it be slow, it’ll still be great, it just takes a little more patience and time. 

If you’re looking to start fermentation as an analog hobby in the new year, our courses are 40% off right now! You can use code NEWYEARS at checkout. (Yes, you learn online, but it’s delicious, long form content + the skills are life long). What you learn empowers you to get off the computer/phone and go ferment some delicious foods and drinks. 

Touching cabbage and dough is just as good as “touching grass” lol 

Let me know if you have questions about our courses or just fermentation in general in the comments!

#fermentation
Yes cooking kills the microbes, but idc. I mean, I Yes cooking kills the microbes, but idc. I mean, I care, but in a “thank you for your service microbes” kinda way. 🫡

Cider braised pork and sauerkraut is a perfect choice for New Year’s or any winter meal! I lovvveee pairing it with butternut squash polenta bc it’s full of vitamin C for cold and flu szn. 

Eating pork and sauerkraut on New Year’s Day is a tradition. And I really do think it brings good luck and prosperity.

Get the recipe on our blog, linked in my profile and in story highlights! 

I’m really looking forward to creating more recipes like this in the new year, to show you all the joys of incorporating ferments into meals and recipes 😌✨ stay tuned! 

#newyear #sauerkraut #fermentation
One Christmas I gifted everyone in my family the N One Christmas I gifted everyone in my family the New York style sourdough bagels and they were thrilled. (The bagels we’re actually way under proofed, but I still gifted them and everyone loved them lol)

You can get the full recipe on my blog! And these can be made with discard and instant yeast or with just active starter.

 All the details are in the 5-star rated recipe on my website. 

#bagels #sourdough
This cookie dough is long-fermented overnight in t This cookie dough is long-fermented overnight in the fridge for the softest, most flavorful, melt-in your mouth sourdough gingerbread cookies.

For Christmas 2025, I tried something new with these cookies. I created a gingerbread sourdough starter to use in this recipe! I made it by feeding some of my established starter a mix that includes molasses and gingerbread spices. I just added the instructions for the gingerbread starter in the notes of my cookie recipe.

Get the full recipe and directions on my website! https://cultured.guru 

You can use the recipe index to see all my Christmas season recipes!

#gingerbread #sourdough
My gingerbread sourdough starter recipe 🎄✨ Like a My gingerbread sourdough starter recipe 🎄✨

Like and save for some fun Christmas sourdough baking! 

I made this up a few days ago to use in my soft sourdough gingerbread cookies. (cookie recipe is in my recipe index on my website!)

#sourdough #gingerbread
Christmas gift feta cheese🧀🎄✨ Part two of my four Christmas gift feta cheese🧀🎄✨

Part two of my four part series on homemade fermented foods to gift this holiday season! This one takes about five days total to prepare, so start now if you plan to gift this one on Christmas. 

GOOGLE “cultured guru feta” to get my feta recipe any time! You can also use the recipe index linked in my bio! 

#fermentation
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