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Healthy Blueberry Muffins

Studded with fresh berries and spiced with warm cinnamon, these Easy Blueberry Muffins use whole wheat flour and natural sweeteners to keep them healthy without sacrificing flavor. They’re the make-ahead breakfast or snack of your dreams!

The Ultimate Healthy Breakfast Muffins

Moist, fluffy and bursting with blueberry goodness, these muffins are a healthy munchie that makes you feel like you’re eating dessert. They’re packed with fiber and nutrients from the whole wheat flour and low in cholesterol thanks to the use of coconut oil rather than butter. On top of that, they use honey instead of sugar, introducing a wealth of health benefits like strengthened immunity and improved digestion.

I love making a double batch of these muffins and keeping one batch in the fridge and the other in the freezer. My family bulldozes through them, so it’s always nice to have a bunch on deck. Whether you need a grab-and-go breakfast or a healthy snack to satisfy your sweet tooth, consider this recipe your pot of gold.

Three moist blueberry muffins on a plate with a butter knife beside them

What You’ll Need

This trusty ingredient lineup makes wholesome muffins that taste even better than the ones from your local bakery. The full amounts are listed in the recipe card near the end of this post.

  • White Whole Wheat Flour: Most of this will go into the muffin batter itself, but one tablespoon will be tossed with the blueberries to prevent them from sinking.
  • Honey: I like the raw and unfiltered kind.
  • Cinnamon
  • Greek Yogurt: You know how sour cream makes muffins extra moist and fluffy? Greek yogurt is a healthier way to achieve the same result!
  • Salt
  • Coconut Oil: Melted and slightly cooled.
  • Vanilla Extract: Use a high-quality extract for the best flavor.
  • Baking Powder
  • Large Eggs
  • Fresh Blueberries

Can I Use Frozen Berries?

Yes, and you don’t even have to thaw them out first! In fact, you shouldn’t – just toss the frozen berries with the flour as usual, fold them into the batter and bake. If you were to thaw them, they’d bleed blue into the muffins and might even make them soggy.

How to Make Whole Wheat Blueberry Muffins

These healthy blueberry muffins come together in about 30 minutes, and less than half of that time is devoted to prep. So even though they’re great for making in advance, they’re also quick enough to whip up on the spot!

  • Heat Oven & Line Pan: Preheat the oven to 375°F. Line a 24-count muffin pan with nonstick muffin liners (you’ll only need 16 liners).
  • Combine Wet Ingredients: Add the honey, greek yogurt, coconut oil, vanilla extract and eggs to a large bowl, whisking until everything is combined.
  • Combine Dry Ingredients: Add the white whole wheat flour, cinnamon, salt and baking powder to a medium-sized bowl.
  • Add to Wet Ingredients: Slowly fold the dry ingredients into the wet ingredients.
A collage of two images with one showing a carton of fresh berries and the other showing the flour-coated berries being folded into the batter
  • Toss Berries With Flour: Set aside half a cup of the blueberries to sprinkle on top of the muffin batter once it’s in the pan. Add the remaining blueberries and 1 tablespoon of white whole wheat flour to a small bowl. Toss to coat all of the berries in the flour.
  • Add to Batter: Gently fold the coated blueberries into the muffin batter.
A muffin tin fitted with liners that are filled with blueberry muffin batter
  • Fill Muffin Tin: Spoon the batter into the prepared muffin pan, filling each liner about 3/4 of the way full.
  • Add Remaining Berries: Sprinkle the top of each muffin with the remaining blueberries.
  • Bake: Bake the muffins for 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Let Cool: Cool the muffins in the pan for 5 minutes before you transfer them to a wire rack to continue cooling.
  • Enjoy! Serve your healthy blueberry muffins warm or at room temperature.
Blueberry muffins inside of a lined cupcake tin with some of the divots filled with blueberries

Tips for Success

Before you start mixing up your muffin batter, take a moment to read over these helpful tips and tricks.

  • Use the Spoon and Level Method: Never scoop a measuring cup directly into a bag of flour – this leads to over-packing. Either spoon in the flour little by little or weigh it out with a food scale.
  • Line or Grease the Muffin Pan: If you don’t have nonstick muffin liners, be sure to grease your muffin tin with cooking spray. Otherwise, you’ll struggle to remove the finished muffins.
  • Remember to Coat the Berries in Flour: The process of coating the blueberries in flour prevents them from sinking to the bottom of the muffins while they bake. It’s a quick and simple step that makes a noticeable difference.
  • Let the Muffins Rest in the Pan: Because these muffins are so moist and tender, they shouldn’t be transferred to a cooling rack as soon as they come out of the oven. They need to rest in the muffin pan for a good 5 minutes to keep them from falling apart.

Mix-In Ideas

As long as you don’t over-mix the batter, you can load up your muffins with any add-ins you’re craving. Here are some foolproof options!

  • Chopped Nuts
  • Lemon, Lime or Orange Zest
  • Blackberries, Raspberries or Strawberry Slices
  • Dark Chocolate Chips
  • Nutmeg
  • Shredded Coconut
  • Chopped Banana
A plate holding three homemade muffins with a stack of two coffee cups in the background

How to Store Homemade Muffins

Cooled blueberry muffins can be kept in an airtight container at room temperature for up to 4 days. I like to line the container with a paper towel to absorb excess moisture, which keeps the muffins from getting soggy. Feel free to warm each muffin in the microwave for a few seconds before you dig in.

Can I Freeze These?

You bet! Simply wrap each muffin in clear wrap and freeze them in a heavy-duty storage bag for up to 2 months. Thaw your muffins in the fridge and bring them to room temperature before enjoying.

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An overhead shot of a pan full of baked muffins with fresh berries scattered about

Healthy Blueberry Muffins

  • Author: Krista
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Total Time: 35 minutes
  • Yield: 16 1x
  • Category: Breakfast
  • Method: Oven
  • Cuisine: American


Studded with fresh berries and spiced with warm cinnamon, these Easy Blueberry Muffins use whole wheat flour and natural sweeteners to keep them healthy without sacrificing flavor. They’re the make-ahead breakfast or snack of your dreams!


  • 2 cups white whole wheat flour
  • 3/4 cup honey
  • 1 teaspoon cinnamon
  • 1 cup plain greek yogurt
  • 1/2 teaspoon salt
  • 1/3 cup coconut oil, melted
  • 1 1/2 teaspoon vanilla extract
  • 2 1/2 teaspoons baking powder
  • 2 large eggs
  • 1 tablespoon white whole wheat flour
  • 2 cups blueberries


  1. Preheat oven to 375°F.
  2. In a large bowl, mix together the wet ingredients – honey, greek yogurt, coconut oil, vanilla extract, and eggs. Whisk together until combined.
  3. To a medium bowl add, white whole wheat flour, cinnamon, salt, and baking powder. Slowly fold the dry ingredients into the wet ingredients.
  4. In a small bowl – combine 1-1/2 cups blueberries & 1 tbsp white whole wheat flour & toss to coat
  5. Gently fold blueberries into the batter.
  6. Spoon the batter into muffin pan filling each hole about 3/4 of the way full (line or spray with cooking spray if not using the cupcake liners)
  7. Sprinkle the top of each muffin with remaining blueberries.
  8. Bake 20 minutes or until toothpick comes out clean.
  9. Cool 5 minutes in pan before transferring to a wire rack to continue cooling – or serve warm


  • Recipe adapted from Kleinworth and Co. Blueberry Streusel Muffins.
  • To Store: Keep cooled muffins in an airtight container at room temperature for up to 4 days. I like to line the container with a paper towel to absorb excess moisture, which keeps the muffins from getting soggy. Feel free to warm each muffin in the microwave for a few seconds before you dig in.
  • To Freeze: Wrap each muffin in clear wrap and freeze them in a heavy-duty storage bag for up to 2 months. Thaw in the fridge and bring to room temperature before enjoying.


  • Serving Size: 1 muffin
  • Calories: 176
  • Sugar: 15 g
  • Sodium: 98 mg
  • Fat: 5 g
  • Saturated Fat: 4 g
  • Carbohydrates: 30 g
  • Fiber: 4 g
  • Protein: 4 g
  • Cholesterol: 24 mg

Keywords: easy blueberry muffins, healthy breakfast muffins, blueberry yogurt muffins

Filed Under:

More Easy Make-Ahead Breakfast Ideas

A collage of two images of blueberry muffins with one showing them on a plate and the other showing them in the pan



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29 comments on “Healthy Blueberry Muffins”

    1. Yes. I’d recommend allowing them to cool and then placing in a freezer safe storage bag. To reheat just wrap in a paper towel and place in the microwave for 45 seconds or let sit out on the counter overnight.

  1. This is my favourite recipe that I found in 2020, I LOVE the blueberry muffins. This is so easy to make and they’re just so, so, tasty!

  2. This recipe is very far off on the wet ingredients. There’s an exceptionally large amount of dry ingredients relative to wet ones and you need to add at least 1 more egg, maybe a little more coconut oil or yogurt or something. There’s zero way, with the recipe listed, you’ll be able to smoothly mix everything together.

  3. Can I substitute frozen blueberries? How about keifer instead of yogurt? That’s all I have right now, but I really want to make these in the morning!

  4. I think there might be something missing from the recipe. Which I combined the dry ingredients with the wet, the batter became really dry and stiff like a bread dough. I feel like either its too much flour or a wet ingredient is missing. I will say that I baked them anyways, and my kiddo still gobbled them up. Great Flavor!

  5. Hello, I am a very disappointed mother. These muffins absolutely suck and belong in the garbage. Cat food tastes better than these wastes of space. My daughter even told me that they tasted like play doh. You should be ashamed of yourself for creating these. Good night,

  6. Avatar photo
    Joanie @ One Dish Kitchen

    You just can’t beat a good blueberry muffin and I love the healthier twist to your recipe. I’ve got a pint of blueberries in my fridge, I’ll be making these muffins with them.

  7. It’s time for me to go get more blueberries, because I have to try your recipe and make these!

  8. Avatar photo
    carrie @ frugal foodie mama

    OMGEE! These muffins look perfect! 🙂 Wish I had a couple of them with my coffee this morning.

    1. The muffins are suuuper gooey. I don’t know if maybe I messed up somewhere because I followed the exact recipe. I was looking for something different, more of a fluffy texture.

    1. These muffins are SO good- they were gone in no time at all! Thank you for sharing your recipe! I have a quick question: I also made your healthy strawberry muffins- Absolutely Loved those as well- can the strawberry muffin recipe be used with blueberries, and the blueberry recipe with strawberries? Or should I not change the fruit/muffin base? I only ask because of ingredients currently in the kitchen! Either way, your recipes are amazing! So flavorful and moist. I also can’t wait to make your zucchini recipes!

      1. Hey Stephanie so pumped your a huge fan of BOTH muffins. Honestly I think you could interchange them. But I’ve never tried it. You’ll have to let me know how it turns out!

  9. Avatar photo
    Kimberly @ The Daring Gourmet

    Those look perfect and I love baking with coconut oil, such a great flavor and texture!

  10. Avatar photo
    Meghan Bassett

    There’s nothing better than a blueberry muffin for breakfast! Pass the coffee and I’ll take two please 😉