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Healthy blueberry muffins, made with applesauce, yogurt, oats and big, beautiful fresh (or frozen!) blueberries, and no added fat or refined sugars. All the taste and texture, none of the guilt!

pile of light brown muffins with blueberries baked inside in brown muffin liners in dark gray dish with 1 1/2 inch sides sitting on blue cloth, with one muffin missing a single bite
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Why I love these muffins

love cake, but I don't usually want something with that much sugar for breakfast. Something with that much sugar doesn't keep me satisfied for long enough.

These healthy blueberry muffins are made with applesauce and plain Greek yogurt, not vegetable oil or butter, and the whole grain goodness of oats.

Moist and tender and easy to make, these naturally gluten free muffins are only lightly sweet and positively bursting with the goodness of blueberries. They're super special right out of the oven (warm berries!), but they also freeze and defrost perfectlyโ€”plus they're easy to make dairy free, too with a nondairy plain Greek-style yogurt.ย 

The rule in my house is that you're on your own for breakfast on the weekend, but during the school week I've got you covered. And make-ahead breakfasts like these muffins and our gluten free banana muffins are always in the freezer, waiting for a quick defrosting in the microwave or toaster oven.

overhead image of ingredients for healthy blueberry muffins in small bowls with names of ingredients in bold black type on blond wood surface

what's in it

Recipe Ingredients

  • Old fashioned rolled oats/oat flour – We use oats to form the base for these healthy muffins by grinding them into oat flour first, before we add any other ingredients. You can, of course, also just begin with an equal amount, by weight, finely sifted oat flour.
  • Coconut palm sugar – This unrefined granulated sugar has a similar flavor to brown sugar, but is much grittier, and doesn't dissolve that well in baking. So be sure to blend it with the oats into a powder. You can use light brown sugar instead.
  • Baking powder and baking soda – These chemical leaveners react with the liquid and acid in these muffins to give our muffins most of their rise. Make sure yours are fresh!
  • Salt – Salt brings out all the flavors of these muffins, and balances the sweet sugar and blueberries.
  • Applesauce – Smooth, processed applesauce adds moisture to these muffins and a tiny bit of structure, from the pectin. Be sure not to use chunky applesauce, or your muffins will be dry and uneven.
  • Plain, Greek-style yogurt – Although you can make these muffins using fat free Greek-style yogurt, you really need the bit of fat in 2% lowfat or 4% whole milk yogurt to help tenderize your muffins. You can replace the plain yogurt with an equal amount of sour cream.
  • Eggs – Eggs provide structure and help these muffins rise. The yolks also add a bit of fat, which these muffins are really low in.
  • Pure vanilla extract – Vanilla brightens and enhances the mild, delicious flavor of these healthy muffins.
  • Blueberries – The star of the show here, blueberries add moisture when they bake in the oven and, of course, that gorgeous summery blueberry flavor to every bite. If you use frozen berries, don't defrost them first, or they'll turn your muffins blue!
  • Cornstarch – Coating your blueberries in a tiny bit of starch helps suspend them in the batter so they don't sink to the bottom of each muffin as it bakes.
pile of whole light brown muffins with some blueberries peeking out of top of each muffin and on side through brown paper wrapping

How to make healthy blueberry muffins

Make the muffin batter

  • In a blender or food processor, process the oats and coconut sugar into a powder, and place them in a large mixing bowl.
  • Add the baking powder, baking soda, salt, and whisk to combine. 
  • Add the applesauce, yogurt, eggs, and vanilla, and mix just until combined.
  • Toss the blueberries with a bit of cornstarch to prevent them from sinking right to the bottom of the batter.
  • Add the berries to the batter, and mix gently until just combined.

Place in muffin tin & bake

  • Divide the batter among the wells of the muffin tin. In my standard muffin tin, the wells are almost completely full of batter.
  • You can add a few more berries to the very top of the batter in each well so they're visible.
  • Bake at 375ยฐF for 5 minutes, then reduce the oven temperature to 325ยฐF for about another 15 minutes. The muffins are done when the muffin springs back after you press a fingertip gently in the center.
  • Allow the muffins to cool first in the tin, then on a wire rack.

My Pro Tip

Expert tips

Use room temperature ingredients

Make sure that your eggs, yogurt, and applesauce are at room temperature before you combine them. That way, they'll combine evenly and won't create clumps that prevent a smooth batter. Your blueberries will be cold if they're frozen, but that's the last thing you're adding to the prepared batter, so it won't harm anything.

Don't defrost frozen blueberries

As with any blueberry muffin, feel free to use either fresh or frozen blueberries for delicious results. If you do the latter, do not defrost frozen blueberries, and keep in mind that they will likely bleed into the batter and turn it a bit purple.

Using frozen berries wonโ€™t affect the taste one bit, though. You can have truly nutritious blueberry muffins all year long!

Coat your blueberries in starch

Coating your blueberries in a bit of starch before mixing them into the batter helps them cling to the batter a bit, and helps keep them from sinking to the bottom of the batter, during baking.

Use muffin liners but grease them

Place greaseproof muffin liners in your muffin tin before adding the batter to make cleanup really easyโ€”and to help give your muffin batter some support as it rises up during baking. Spray the liners with a light coating of cooking oil spray, too. Lowfat muffins like these tend to stick to their liners.

Don't overmix the batter

Be careful not to overblend the batter. Oat flour has a tendency to get tough if you overmix or overblend it before baking.

For fluffier muffins, add starch

Try replacing about 25 grams of the oat flour with 25 grams of cornstarch for a more stable muffin with a more tender crumb.

Raw batter for healthy blueberry muffins in a bowl

substitutions

Ingredient substitutions

Dairy free

In place of regular Greek-style yogurt, you can definitely use a nondairy plain yogurt or sour cream substitute. If you use plain yogurt, be sure to drain it until itโ€™s of a similar consistency to Greek-style yogurt, and then measure the ingredient by weight. 

Egg free

Since this recipe contains 2 eggs, you should be able to replace them with some success using your favorite egg substitute. My favorite is one โ€œchia eggโ€ (1 tablespoon ground white chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel) per standard egg. Flax eggs should work, but they will add more unwanted flavor.

Applesauce

The applesauce in this recipe provides structure, sweetness, and tenderness to the muffins. The muffins donโ€™t taste at all like applesauce. If youโ€™d prefer to use bananas, try my recipe for banana oatmeal muffins.

Oat free

Since they're ground into a fine powder for use in this recipe, you can substitute for oats with quinoa flakes. I've tried this recipe with that substitution, by weight, and although the muffins were a tiny bit more fragile, the recipe worked great.

Blueberries

In place of blueberries, I think these muffins would be great with an equal amount, by weight, of chopped strawberries or raspberries. You can also try frozen mixed berries as long as they're all relatively small in size (nothing larger than a raspberry). And remember not to defrost frozen berries first!

Sugar free

If you prefer to use unrefined sugars, go with the coconut palm sugar. It does have a coarse grain, though, so be sure to blend it along with the oats into a fine powder.

You can use an equal amount by weight of light brown sugar (which is what I use in the video). You could probably also use a brown sugar alternative, like Truvia brown sugar replacement.

I havenโ€™t tried that, though, so youโ€™ll have to experiment and please comment below and let us know how it went.

FAQs

Can I use store-bought oat flour instead of grinding my own oats?

Yes! If you already have oat flour on hand, measure out 225 grams by weight of packaged oat flour. I like Gold Medal brand oat flour for its quality and availability.

How do I make sure my muffins aren't dry?

If you want to make sure your muffins are moist, don't cut back on the sugar (sugar is a tenderizer and moisturizer in baking) and use Greek yogurt with at least 2% fat (not fat free) or sour cream. Fat is a tenderizer, too.

How do I know when my muffins are done baking?

The “doneness” test in this recipe requires you to bake the muffins until their tops are nicely domed, and they spring back when pressed gently with a finger.

Have you tried making them as mini muffins?

I haven't tried that, but I think it would work well. Be sure to use mini muffin liners and grease them for best results and reduce the baking time. I would bake at 375ยฐF for 3 minutes, then reduce to 325ยฐF until done (about another 10 minutes).

What if I wanted to make this as a loaf instead of muffins?

I don't recommend trying to make this same batter as a loaf instead of muffins. It doesn't have the proper structure to support baking in a single standard loaf pan. Mini loaf pans might work, though!

Can I replace the eggs with more applesauce?

No, more applesauce will make the batter too wet and not provide the structure and binding of eggs. For making these muffins egg-free, please see the substitutions section above.

Can sorghum flour be used instead of oat flour?

I haven't tried that substitution, so I don't know! You can replace the oat flour with quinoa flakes. I think the recipe might also work with finely ground blanched almond flour in place of oat flour, too.

Can I add bananas to this recipe?

You may be able to replace all or part of the applesauce with an equal amount, by weight, of mashed ripe bananas. Those substitutes often work well, so it's worth a try!

Can you make this recipe without the yogurt?

You can replace the Greek style plain yogurt with an equal amount, by weight, of sour cream (dairy or nondairy). If you only have plain yogurt that isn't Greek-style, strain it of liquid until it reaches the consistency of sour cream or Greek yogurt.

Can you double the recipe?

Yes! Just change the yield in the recipe below to make 24 muffins, or click the “2X” button to double all the ingredients. Bake in 2 standard 12-cup muffin tins as directed.

Can I make these with wheat flour?

You might be able to replace the oat flour with conventional whole wheat flour or whole wheat pastry flour. Unlike our classic gluten free blueberry muffins which are made with an all purpose gluten free flour, these are made with a single whole grain (oat flour) and a regular all purpose flour probably would not work.

pile of light brown muffins with blueberries in a dark gray round dish with fluted edges with some fresh whole blueberries around the muffins, and one muffin with a bite taken revealing baked bright berries inside

Make ahead/leftovers

Storage Instructions

For short term storage, these muffins will stay fresh for about 2 days on the kitchen counter if they're wrapped individually with plastic wrap or in a sealed container.

Freezing

For longer storage, place them in a single layer on a rimmed baking sheet until frozen, then pile them into a large ziptop bag until you're ready to enjoy them.

Defrosting/refreshing

You can allow these muffins to defrost at room temperature on the counter for about 30 minutes or microwave for about 25 seconds. To refresh and serve warm, sprinkle the defrosted muffin lightly with lukewarm water and place in the toaster oven on toast, or at 300ยฐF for about 5 minutes.

Healthy Blueberry Muffins Recipe

4.95 from 20 votes
Prep Time: 15 minutes
Cook Time: 20 minutes
Resting time: 5 minutes
Total Time: 40 minutes
Yield: 12 muffins
These healthy blueberry muffins are tender, moist and packed with blueberries. Made with oat flour and no butter or oil!

Equipment

  • Blender or food processor
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Ingredients 

  • 2 ยผ cups (225 g) old fashioned rolled oats, (gluten free if necessary) (See Recipe Notes)
  • ยฝ cup (80 g) granulated coconut palm sugar, (or light brown sugar)
  • 1 ยฝ teaspoons baking powder
  • ยฝ teaspoon baking soda
  • ยผ teaspoon kosher salt
  • 1 cup (240 g) smooth applesauce, at room temperature
  • ยฝ cup (114 g) plain Greek-style yogurt, (1%, 2%, or even 0% fatโ€”but I prefer 2%), at room temperature
  • 2 (100 g (weighed out of shell)) eggs, at room temperature, beaten
  • 1 teaspoon pure vanilla extract
  • 6 ounces fresh (or frozen) blueberries, plus more for on top (optional)
  • 2 teaspoons (6 g) cornstarch, (or arrowroot)

Instructions 

  • Preheat your oven to 375ยฐF. Line the wells of a standard 12-cup muffin tin.
  • Spray the liners with a light coating of cooking oil spray to prevent the liners from sticking to these lowfat muffins. Set the prepared pan aside.
  • In a blender (or food processor fitted with the steel blade), place the oats and process into a fine powder. If youโ€™re using coconut palm sugar, place that in the blender, too, and process it too.
  • Place the oat flour, sugar, baking powder, baking soda, and salt in a large mixing bowl, and create a well in the center.
  • Add the applesauce, yogurt, eggs, and vanilla, and mix until just combined.
  • Place the blueberries in a small bowl and toss them in the 2 teaspoons of cornstarch.
  • Add the blueberries with the added cornstarch to the muffin batter, and fold the blueberries gently into the batter until they're evenly distributed throughout. The batter will be thick but very soft.
  • Allow the batter to sit briefly after mixing. This will allow it to thicken a bit and make transferring it to the muffin tin a bit easier.
  • Divide the batter evenly among the prepared wells of the muffin tin. Shake the tin back and forth to evenly distribute the batter in the wells.
  • Add a few (optional) fresh or frozen whole blueberries to the batter in the tops of the wells. You can use up to 1 additional ounce of berries total. Press gently to help the berries sink a bit into the batter.
  • Place the tin in the center of the preheated oven and bake for 5 minutes.
  • Reduce the oven temperature to 325ยฐF and continue to bake until the tops of the muffins are nicely domed, and they spring back when pressed gently with a finger. This usually takes another 13 to 15 minutes.
  • Remove the muffin tin from the oven and allow to cool for about 10 minutes in the tin before transferring to a wire rack to cool completely.

Video

Notes

Oats or oat flour.
Since you are grinding the oats into oat flour, you can begin with 225 grams, by weight, of oat flour. That's approximately 1 7/8 cups oat flour.
Nutrition information.
The approximate nutrition information does not include any (optional) additional blueberries beyond the 6 ounces specifically called for in the recipe.

Nutrition

Serving: 1muffin | Calories: 116kcal | Carbohydrates: 21g | Protein: 4g | Fat: 2g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 0.003g | Cholesterol: 28mg | Sodium: 176mg | Potassium: 92mg | Fiber: 2g | Sugar: 8g | Vitamin A: 59IU | Vitamin C: 2mg | Calcium: 54mg | Iron: 1mg

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

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A close up of a healthy blueberry muffin broken in half
Image of a muffin tin with healthy blueberry muffins.
Healthy blueberry muffin ingredients, batter raw in muffin tin, baked in tin and baked on a plate
Closeup image of broken blueberry muffin and overhead image of broken blueberry muffin with more blueberries

About Nicole Hunn

Hi, Iโ€™m Nicole. I create gluten free recipes that really work and taste as good as you remember. No more making separate meals when someone is GF, or buying packaged foods that arenโ€™t good enough to justify the price. At Gluten Free on a Shoestring, โ€œgood, for gluten freeโ€ just isnโ€™t good enough!

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33 Comments

  1. Marie says:

    5 stars
    These muffins were so moist and chewy. I will be making these over and over. Iโ€™m will try with apples, bananas and other fruits as well.

  2. tiffany says:

    Can I use mashed RIPE bananas instead of applesauce, and omit the sugar?

    Please let me know, thank you so much!!

    1. Nicole Hunn says:

      No, you canโ€™t omit the sugar and have the recipe turn out.

  3. Sally says:

    5 stars
    I substituted fresh cranberries for the blueberries and added orange zest and substituted orange juice for the vanilla they are very tasty.

  4. Connie says:

    4 stars
    In the written instructions, you do not mention adding the baking powder, baking soda and salt… Most of us know to add them into the dry ingredients before the wet ingredients but you might want to add that between steps 2 and 3 (would you put them in the blender or in the bowl? I added mine to the bowl before the applesauce. [By the way, I substituted banana for applesauce and they came out great].

    1. Nicole Hunn says:

      Oh my gosh, Connie, thank you so much for pointing that out! I’ve added those ingredients to the instructions just where you said. Thank you again!

  5. Karen says:

    I made these for the second time–only this time i lost my mind and forgot to add yogurt. Surprisingly, they were still amazing!! Thank heavens as I just made a double batch!

    1. Nicole Hunn says:

      Now that’s surprising, Karen! I mean, I like my recipes to be solid enough as to be relatively flexible, but that’s quite a difference!

  6. Naomi says:

    Oh how I want some of these muffins! One question first, though: did you use sweetened or unsweetened applesauce, or does it matter?

    1. Nicole Hunn says:

      I always use unsweetened smooth applesauce, Naomi! You can of course use sweetened, but there’s no need. :)