Healthy Blueberry Muffins

Healthy Blueberry Muffins

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

A close up of a healthy blueberry muffin broken in half

A truly good-for-you breakfast, the easy way

It’s easy to fool ourselves into thinking that muffins are better for you than cupcakes. They’re breakfast food, after all. But when they’re filled with refined flours and sugars and unhealthy fats, they’re really just, well, cake.

Please don’t misunderstand, because I love cake. But I don’t love giving my children cake for breakfast, especially on a school morning. So healthy muffins are really a sweet spot (haha pardon the pun). 

And these healthy blueberry muffins are made with applesauce and plain Greek yogurt, not vegetable oil or butter, and the whole grain goodness of oats. I love the idea of making a fresh, homemade breakfast every day, but there’s just no way that’s happening every day.

Moist and tender, these insanely delicious 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 perfectly. 

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 are always in the freezer, waiting for a quick defrosting in the microwave or toaster oven.

Image of a muffin tin with healthy blueberry muffins.

How to make these whole grain healthy blueberry muffins

When I first developed this recipe, I always made the batter by dumping all of the ingredients other than the blueberries in a blender. That method still works!

Simply add the wet ingredients (applesauce, yogurt, eggs, vanilla) first, then followed by the sugar and then the dry ingredients (oats, baking powder, baking soda, salt). Then, fold in the blueberries, portion among the muffin wells, and bake.

I’ve switched up the directions below, though, to call for grinding the oats first, alone (or with the sugar if using coconut palm sugar, which tends to have a coarse grain). That way, you don’t risk overprocessing the batter which can lead to tough muffins.

Plus, whenever I make a wet batter in a blender, I feel like I’m leaving a few tablespoons of the precious batter behind in the machine. It’s a lot easier to get dry ingredients out of a blender!

Simply blend the oats (with or without the sugar) into a powder and place them in a large mixing bowl. Add the sugar (if not already added), then the baking powder, baking soda, salt, and whisk to combine. 

Add the wet ingredients and mix just until combined. Add the berries, tossed with a tiny bit of starch to prevent them from sinking right to the bottom of the batter, place in the muffin wells and bake.

Raw batter for healthy blueberry muffins in a bowl

Fresh or frozen blueberries

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

Using frozen berries won’t affect the taste one bit, though. You can have truly nutritious, naturally gluten free blueberry muffins all year long!

Healthy blueberry muffin ingredients, batter raw in muffin tin, baked in tin and baked on a plate

Can you make the muffins without oats?

Oats are appropriate on a gluten free diet, but you have to decide what is appropriate for you and your family. Since they’re ground into a fine powder for use in this recipe, you should be able to replace the oats here with quinoa flakes. 

I haven’t tried this particular recipe with quinoa flakes in place of the oats, but I think they’d work great. I was about to try making them just the other day and realized I was out of quinoa flakes so I just went ahead with another batch of the oat-based recipe. My 3 teenagers will plow through another dozen muffins in no time!

A plate with a cup of coffee, with a blueberry muffin overhead

Ingredients and substitutions


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 it’s of a similar consistency to Greek-style yogurt, and then measure the ingredient by weight. 


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 “chia egg” (1 tablespoon ground white chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel) per standard egg. 


The applesauce in this recipe provides structure, sweetness, and tenderness to the muffins. The muffins don’t taste at all like applesauce. If you’d prefer to use bananas, try my recipe for banana oatmeal muffins.


Please see the discussion above about oats!


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, since I couldn’t find my treasure trove of coconut sugar). You could probably also use a brown sugar alternative, like Truvia brown sugar replacement.

I haven’t tried that, though, so you’ll have to experiment and please comment below and let us know how it went.


Closeup image of broken blueberry muffin and overhead image of broken blueberry muffin with more blueberries

Like this recipe?

Prep time: Cook time: Yield: 12 muffins


2 1/4 cups (225 g) certified gluten free old fashioned rolled oats (or regular rolled oats if GF is not an issue)

1/2 cup (80 g) granulated coconut palm sugar (or light brown sugar)

1 1/2 teaspoons baking powder

1/2 teaspoon baking soda

1/4 teaspoon kosher salt

1 cup (240 g) smooth applesauce, at room temperature

1/2 cup (114 g) plain Greek-style yogurt (1%, 2% or 0% fat—but I prefer 2%), at room temperature

2 eggs (100 g, weighed out of shell) at room temperature, beaten

1 teaspoon pure vanilla extract

5 ounces fresh (or frozen) blueberries

2 teaspoons (6 g) cornstarch (or arrowroot)


  • Preheat your oven to 325°F. Grease or line the wells of a standard 12-cup muffin tin, and set it aside.

  • In a blender (or food processor fitted with the steel blade), place the oats and process into a fine powder. If you’re using coconut palm sugar, place that in the blender, too, and process it too. Create a well in the center of the dry ingredients and add the applesauce, yogurt, eggs, and vanilla, and mix until just combined. Add the blueberries tossed in cornstarch, and mix gently until the blueberries are evenly distributed throughout the batter. The batter will be thick but very soft. 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.

  • Place the tin in the center of the preheated oven and bake until the tops of the muffins are nicely domed and they spring back when pressed gently with a finger, about 18 minutes. Remove from the oven and allow to cool for about 10 minutes in the tin before transferring to a wire rack to cool completely.

  • Adapted from my Healthy Banana Breakfast Muffins. Originally published on the blog in 2016. Some photos, video, some text new; recipe method changed for sake of simplicity and best results.


Comments are closed.

  • Karen
    August 7, 2019 at 11:29 AM

    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!

    • Nicole Hunn
      August 7, 2019 at 1:47 PM

      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!

  • Naomi
    August 4, 2019 at 11:48 PM

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

    • Nicole Hunn
      August 5, 2019 at 11:54 AM

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

  • Nancy
    July 31, 2019 at 10:29 PM

    Thank you for this recipe, Nicole. These muffins are delicious! For years I have been searching for a recipe for blueberry muffins that aren’t like cake, but taste good. This is it! I am no longer gluten free (after a year to see if my Chronic Fatigue symptoms could be misdiagnosed Celiac), but still using your recipes. Really, thank you. My husband loved them too!

    • Nicole Hunn
      August 1, 2019 at 1:48 PM

      That’s exactly what this recipe is, Nancy! Muffins that aren’t cake in disguise, and actually taste good. So glad you and your husband are enjoying them—and sticking around after no longer needing to be GF. :)

  • Milvi
    July 28, 2019 at 5:32 PM

    As a greek yogurt substitution (trying to switch to plant based of late), I tried vegan mayonnaise (1:1) and aquafaba (6 tbsp of reduced af) for the egg substitution. End result was super moist muffin that was delicious! It didn’t puff up much, so next time I’ll try to whip those ‘eggs’ up a bit first. Great recipe, as always!!

    • Nicole Hunn
      July 29, 2019 at 6:21 AM

      Thanks for letting us know how it turned out, Milvi!

  • Diane
    July 28, 2019 at 9:59 AM

    My husband is very critical. His usual comments are “I’ve had worse” or “not terrible.” But for these, as he’s stuffing another one in his mouth, “these muffins are really good!” I agree ;) Easy to make and YUMMY! Thanks again!

    • Nicole Hunn
      July 28, 2019 at 1:47 PM

      That’s absolutely hysterical, Diane! That sounds like it might just be the best compliment we (together) ever got!!

  • GF Mum
    July 27, 2019 at 7:45 PM

    Hi Nicole,
    We made your banana oat muffins last week, so we had to make these to try them out. Delicious! Everyone loved them. I really appreciate a healthy muffin recipe!

  • Patsy
    July 27, 2019 at 1:13 PM

    Could you monk Duite or swerve for the sygar

    • Nicole Hunn
      July 27, 2019 at 6:37 PM

      Hi, Patsy, please see the ingredients and substitutions section for all the information I have on sugar replacements and other ingredients!

  • Vivian Howard
    July 27, 2019 at 10:11 AM

    Hello, Looking forward to making these. Can I use Quick Cooking Oats instead of Old Fashioned Oats?
    Or maybe oat flour since I do have some of that. If so, how much?

    • Nicole Hunn
      July 27, 2019 at 11:22 AM

      Hi, Vivian, sure you can use any sort of oats, since you need them processed into a flour anyway. Just measure by weight!

  • Heather Storey
    June 20, 2016 at 10:16 AM

    Thanks for the great sounding recipe blueberry is my all time fave. I do have a challenge though as down here in Australia there is no such thing as gluten free oats – could I substitute brown rice flour or another combination? I feel that we miss out on such a lot of nice sounding American recipes. I have 3 of your recipe books and I think they’re great.

  • Rebecca S.
    June 16, 2016 at 1:25 PM

    I just made these. I didn’t have ANY blueberries, so I used chocolate chips instead. But with a healthy batter like this? I didn’t mind the added sugar. My kids loved them. Thanks for such an easy recipe. And in the blender! Mind blown.

    • June 16, 2016 at 4:44 PM

      Oh I totally agree, Rebecca. The chips are warranted. So glad you loved the muffins!

  • roastedroot
    June 16, 2016 at 9:45 AM

    These muffins look fabulous! I feel like muffins > cupcakes any ol day, and when they’re actually healthy? Even better. I’m fantasizing about enjoying these while drinking tea on the porch…perfection!

    • June 16, 2016 at 10:23 AM

      Can’t argue with that visual, Julia! :)

  • yvonne
    June 15, 2016 at 2:20 PM

    If I use almond milk instead of the yogurt,what adjustments to the liquid do I make? Thanks

    • June 16, 2016 at 10:22 AM

      Yvonne, you can’t use almond milk in place of yogurt. It’s just too thin. If you need a dairy free option, try straining coconut milk yogurt until it’s the consistency of sour cream.

      • yvonne
        June 16, 2016 at 11:03 AM

        Thanks. I will probably not be able to make this recipe. Somehow, no matter what kind of yogurt (coconut, almond, etc) I try , I super sensitive GI track can’t tolerate them. Still, bunches of thanks for your prompt reply. I might just use additional applesauce knowing that the taste will not be as good, but I can still make my ” quasi” goodies ;)

        • Rebecca S.
          June 16, 2016 at 11:40 AM

          What about coconut milk from the can, after refrigerating overnight, grab the hardened part and then add bits of the liquid part until it’s the consistency of yogurt?

        • yvonne
          June 16, 2016 at 1:05 PM

          You are so sweet to think of an alternative. the canned coconut is not tolerated. But, really THANKS!

        • Claire
          June 17, 2016 at 9:37 PM

          You could try low fat cottage cheese as odd as that sounds. My aunt has trouble with fat content and she’s been using that for >15years. You’d probably have to mix it with some more applesauce to ensure the moisture content is the same or almond milk. Though cottage cheese is pretty moist.
          Hopefully you can try this alternative

        • yvonne
          June 17, 2016 at 10:08 PM

          Agree at idea but I am lactose and soy intolerant since I was an infant

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