Quick & Easy Sourdough Mini Muffins (Little Bites copycat) 

4.48 from 90 votes
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Sourdough mini muffins are a delicious homemade alternative to Little Bites muffins. Soft, tender, and moist, and customizable with plenty of mix-in options. Plus, they come together in under 30 minutes and are incredibly easy to make. Perfect for breakfast, snacks, or lunchboxes, they’re a treat the whole family will love.

mini sourdough muffins in a brown bowl topped with strawberries, blueberries, sprinkles or chocolate chips
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In honor of back-to-school season, I’ve been working on homemade sourdough versions of your favorite childhood snacks. From Cheez-Its, Goldfish, and animal crackers to granola bars, oatmeal cream pies, and now mini muffins, there’s something for everyone.

Why You’ll Love This Recipe 

  • Quick & Easy- All you need is about 20 minutes from start to finish to make this muffin recipe. With minimal dishes and common pantry ingredients, you can whip up a batch of mini muffins with ease. 
  • Made with good-for-you ingredients- This recipe uses greek yogurt for extra protein and moisture and is sweetened with honey. Plus, it uses up some of our favorite ingredient— sourdough discard. 
  • Customizable- From fruits like strawberries, blueberries, raspberries to mini chocolate chips to sprinkles, the mix-in possibilities for this recipe are endless.
sourdough mini muffins with chocolate chips in a brown bowl with chocolate chips sprinkled around

Ingredients 

  • Butter: This recipe calls for melted butter. If you use salted butter, you can omit the salt in the recipe. 
  • Greek Yogurt: I used plain non-fat greek yogurt, but you could also use whole milk greek yogurt or a flavored variety.
  • Sourdough Discard: Discard refers to unfed sourdough starter. I use sourdough discard straight from the fridge—no need to bring it to room temperature.
  • Honey: This can be substituted with maple syrup or cane/granulated sugar.
  • Milk: I use whole milk, but any kind will work. You can also use a dairy-free alternative.
  • Vanilla Extract: Adds flavor to the recipe.
  • Egg: Acts as a binder for the muffin.
  • Salt: Adds flavor to the recipe. This can be omitted if using salted butter.
  • Baking Powder: This is what leavens the muffins.
  • Baking Soda: I recently started adding this to make the muffins fluffier.
  • All-Purpose Flour: Works great for this recipe. You could also try using some whole wheat flour in place of the all purpose flour for extra nutrients.
brown bowl filled with mini muffins with blueberries and strawberries

Substitutions 

  • Greek Yogurt: You can replace this with sour cream or a different type of yogurt.
  • Sourdough Discard: Use active sourdough starter in place of discard. If you don’t have a sourdough starter, add an extra 1/4 cup of milk to the recipe.
  • Milk: You can substitute dairy-free milk if needed.

Mix-Ins for the Sourdough Mini Muffins

When adding mix-ins to these mini muffins, the options are endless. I recommend adding about 1 cup of mix-ins to the batter. If you want a variety of flavors, add the mix-ins individually after the muffin batter is divided in the muffin tin. Use a toothpick to mix in the fruit so it’s incorporated throughout the muffin.

For a healthier snack, mixing in fruit is a great option. Use fresh blueberries, strawberries, raspberries, blackberries, apples, or whatever you prefer. Dice the fruit into small bite-sized pieces (if your blueberries are small, you can add them whole) and fold into the batter. If you don’t have fresh fruit available, you can also use dehydrated or frozen fruit. When using frozen fruit, you don’t need to defrost it beforehand.

For a more dessert-like option, you can add sprinkles or mini chocolate chips. You could also add extra seasonings if you want, like cinnamon and nutmeg.

How to Make Sourdough Mini Muffins

Preheat the oven to 350°F.

In a large mixing bowl, whisk together the honey, melted butter, milk, sourdough discard, greek yogurt, vanilla extract, and egg until combined.

In a separate bowl, mix together the dry ingredients: flour, baking powder, baking soda and salt. Add to the wet ingredients mixture and stir until just combined.

muffin batter

Fold in your mix-ins of choice, or if you want a variety of mix-ins, add them individually to the batter once it’s in the muffin pan.

batter in muffin tins

Grease a mini muffin tin and evenly divide the batter among the 24 muffin cups, scooping about 1 1/2 tablespoons of batter to each. Alternatively, you can line the muffin tin with paper liners.

mini sourdough muffins in a muffin tin topped with strawberries, blueberries, sprinkles or chocolate chips

Bake for about 12 minutes or until a toothpick comes out clean.

Cool on a cooling rack and enjoy. Store in an airtight container on the counter for the first 2 days and then in the fridge to avoid mold.

Frequently Asked Questions

Can I long ferment this recipe?

Yes! If you want the health benefits of fermenting your batter, you can leave it overnight in the fridge.

Do muffins freeze well?

Muffins freeze very well. Place the mini muffins in a single layer on a cookie sheet and flash freeze them for one hour or until frozen solid. Then, place the muffins in a freezer-safe ziplock bag or another airtight container. They will stay good in the freezer for up to 3 months. To defrost, simply remove a few from the freezer and pop them in the microwave or let them thaw on the counter.

Can I make full-sized muffins?

Yes, but they won’t yield a full set of 12 muffins. You will also need to extend the baking time.

Is it possible to use active starter instead of discard?

You can use active sourdough starter in place of sourdough discard; either one will work.

mini muffins in a muffin tin

Storage Instructions

Once the mini muffins are completely cooled, store them in an airtight container on the counter for the first 2 days. After that, I recommend placing them in the fridge to avoid them molding as they do not have preservatives or excess amounts of sugar. You can also freeze the mini muffins for three months, as explained in the previous section.

Best Tips

  • Don’t overmix the batter, it will lead to tough muffins.
  • Remove the muffins from the pan to cool.
  • Use a toothpick to mix in any mix-ins added after the muffins were scooped into the muffin tin.
sourdough mini muffins with chocolate chips in a brown bowl
4.48 from 90 votes

Sourdough Mini Muffins

These sourdough mini muffins are a quick and easy homemade alternative to Little Bites muffins. They are soft, moist and can be made with so many different mix-ins. They are lightly sweetened with honey and have greek yogurt for added protein. Perfect for breakfast, snacks, or lunchboxes, they’re a treat the whole family will love.
Prep: 10 minutes
Cook: 12 minutes
Total: 22 minutes
Servings: 24 mini muffins
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Ingredients 

  • 80 grams honey, ⅓ cup
  • 60 grams butter, melted, ¼ cup
  • 120 grams milk, ½ cup
  • 60 grams sourdough discard, ¼ cup
  • 80 grams plain greek yogurt, ⅓ cup
  • 5 grams vanilla extract, 1 teaspoon
  • 1 large egg, 50 grams
  • 245 grams all-purpose flour, 1 ¾ cup
  • 5 grams baking powder, 1 teaspoon
  • 3 grams baking soda, ½ teaspoon
  • 3 grams salt, ½ teaspoon
  • Optional mix-ins: chocolate chips, fruit, sprinkles

Instructions 

  • Preheat the oven to 350℉.
  • Mix together the honey, melted butter, milk, sourdough discard, greek yogurt, vanilla extract, and egg until combined.
    80 grams honey, 60 grams butter, melted, 120 grams milk, 60 grams sourdough discard, 80 grams plain greek yogurt, 5 grams vanilla extract, 1 large egg
  • In a separate bowl mix together the flour, baking powder, baking soda and salt. Add to the wet ingredients and stir until just combined.
    245 grams all-purpose flour, 5 grams baking powder, 3 grams baking soda, 3 grams salt
  • Fold in mix-ins of choice or if you want a variety of mix-ins add them individually to the batter once in the muffin pan.
    Optional mix-ins: chocolate chips, fruit, sprinkles
  • Grease a mini muffin pan and evenly divide the batter among the 24 muffin cups, adding about 1 1/2 tablespoons of batter to each.
  • Bake for about 12 minutes or until a toothpick comes out clean.
  • Cool on a cooling rack and enjoy. Store in an airtight container on the counter.

Notes

  • This recipe was updated on 1/27/25 to add baking soda which helps produce a lighter and fluffier muffin.
  • These muffins are not overly sweet but can become sweeter with the mix-ins added in.
  • Be careful not to overmix the batter as it can make the muffins tough.
  • Once baked, remove the muffins from the pan and cool on a cooling rack.
  • If you are doing the same mix-in for all the muffins add about 3/4 – 1 cup of the mix-ins to the batter before scooping it out, depending on how much of the mix-in you want.
  • After the first 2 days keep these in the fridge to avoid mold. They will get tough, so pop them in the microwave for 10 seconds and they taste like they just came out of the oven, soft and moist. You can also flash freeze some on a sheet pan for an hour and then place in a freezer-safe bag for up to 3 months.

Nutrition

Serving: 1muffin, Calories: 76kcal, Carbohydrates: 11g, Protein: 2g, Fat: 2g, Saturated Fat: 1g, Polyunsaturated Fat: 0.2g, Monounsaturated Fat: 1g, Trans Fat: 0.1g, Cholesterol: 13mg, Sodium: 127mg, Potassium: 28mg, Fiber: 0.3g, Sugar: 3g, Vitamin A: 81IU, Vitamin C: 0.02mg, Calcium: 26mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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About Emily Christensen

Welcome to Country Roads Sourdough! Here, I share my no-stress approach to making sourdough bread. I’m so excited to share my time-saving hacks, spill my best-kept tips and tricks, and whip up a bunch of my favorite sourdough recipes with you.

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40 Comments

  1. countryroadssourdough says:

    Both delicious options. Glad you liked them. Thanks for the review.

  2. countryroadssourdough says:

    So glad you enjoyed them!

  3. Elizabeth says:

    5 stars
    My grandsons and friends loved these with chocolate chips and now requesting blueberries!!

  4. Meghan says:

    5 stars
    These are just right! Not too sweet but still a nice treat. I added fresh blueberries and chocolate chips separately once they were in the muffin tins and made sure not to over mix. They were nice and fluffy 🙂

  5. Melissa says:

    How do you think these would turn out with vanilla protein powder added in?

    1. countryroadssourdough says:

      I think you could get away with doing something like 75% flour 25% protein.

  6. Emily says:

    5 stars
    These muffins came out really well, they were easy and tasted amazing! My kids loved them too!

  7. Amy says:

    2 stars
    I could never get the middle cooked. I had to throw them in the trash! I have used yogurt a long time ago in a recipe and same thing. So I won’t be using yogurt again.

  8. Shae says:

    4 stars
    My muffins wouldn’t cook through but the outsides were tough. Maybe I over mixed it. I also only have medium size muffin tins, maybe that was it too? Next time I’ll try mixing less and see if it helps. I added cinnamon which gave them a nice flavor.

  9. Katy says:

    5 stars
    They came out great. Not dense at all. I used the weight measurements in recipe. Not too sweet my toddler loved them.

  10. Audra says:

    4 stars
    I’m out of butter but really want to make these for my kids, can I substitute avocado oil for butter?