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Healthy Blueberry Muffins

These healthy blueberry muffins are golden, fluffy, moist and delicious! No one will guess this recipe is made with 100% whole wheat flour and naturally sweetened with honey or maple syrup.

Updated by Kathryne Taylor on August 30, 2024

885 Reviews

2049Comments

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Would you look at those blueberry-studded beauties? These blueberry muffins are golden on top, and moist and fluffy on the inside.

Best of all, they’re bursting with jammy blueberry flavor. These are my favorite homemade blueberry muffins, and it’s about time you met them.

These healthy blueberry muffins are easy to make, too. Forget those box mixes! You can make these wholesome muffins from scratch with basic grocery store ingredients. No special equipment required.

What makes these blueberry muffins healthy?

These muffins are more healthy than your average blueberry muffins. They’re made with 100 percent whole wheat flour (I used white whole wheat flour, which you can hardly taste). Whole wheat flour offers redeeming whole grain nutrients and extra fiber.

The muffins are also naturally sweetened with honey or maple syrup, which lend subtle honey or maple flavor to the muffins. They’re lower in overall sugar content compared to coffee shop muffins.

Last but not least, I used Greek yogurt instead of sour cream, which lends the same irresistible tang but with more protein and less fat. I don’t think that yogurt passes for sour cream on tacos, but it totally works in muffin recipes.

Blueberry Muffin Recipe Tips

You can make these muffins with fresh or frozen blueberries. Do not defrost frozen blueberries before using; just stir the frozen blueberries into the batter as directed.

Tossing the blueberries with one teaspoon of flour prevents them from sinking to the bottom. This way, you can use a full cup of blueberries without risking the integrity of the muffins.

Sprinkling 1 tablespoon of raw sugar on top of the muffins before baking yields deliciously sweet, crackly muffin tops. You can buy raw sugar in the sugar aisle of most grocery stores these days, or just grab a few extra raw sugar packets from your go-to coffee shop (I won’t tell).

These muffins taste best after they’ve had time to cool completely. Or better yet, let them rest for a couple of hours at room temperature before serving. This is true for most baked goods!

Recommended Equipment

I love this sturdy, made-in-the-USA muffin pan (affiliate link). I don’t ever have to grease it, thanks to the silicone non-stick coating. Clean-up is a breeze, too. I’ve never had to soak or scrub on this pan.

Watch How to Make Blueberry Muffins

Love these muffins?

Here are more of my favorite naturally sweetened, whole-wheat muffin recipes!

• Healthy Apple Muffins
• Healthy Banana Muffins
• Healthy Carrot Muffins
• Healthy Raspberry Muffins
• Healthy Pumpkin Muffins
• Healthy Zucchini Muffins

Please let me know how these muffins turn out for you in the comments! I’m always so eager for your feedback.

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Healthy Blueberry Muffins

• Author: Cookie and Kate
• Prep Time: 13 minutes
• Cook Time: 22 minutes
• Total Time: 35 minutes
• Yield: 12 muffins 1x

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.8 from 885 reviews

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These healthy blueberry muffins are golden, fluffy, moist and delicious! No one will guess this recipe is made with 100% whole wheat flour and naturally sweetened with honey or maple syrup. Recipe yields 12 muffins.

Ingredients

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• 1 ¾ cups plus 1 teaspoon white whole wheat flour or regular whole wheat flour
• 1 teaspoon baking powder
• ½ teaspoon baking soda
• ½ teaspoon fine sea salt
• ¼ teaspoon ground cinnamon (optional)
• ⅓ cup melted coconut oil or extra-virgin olive oil
• ½ cup honey or maple syrup
• 2 eggs, preferably at room temperature
• 1 cup plain Greek yogurt*
• 2 teaspoons vanilla extract
• 1 cup (6 ounces) blueberries, fresh or frozen
• 1 tablespoon turbinado sugar (also called raw sugar), for sprinkling on top

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Instructions

1. Preheat the oven to 400 degrees Fahrenheit. If necessary, grease all 12 cups on your muffin tin with butter, coconut oil or cooking spray (my pan is non-stick and doesn’t require any grease).
2. In a large mixing bowl, combine 1 ¾ cups of the flour with the baking powder, baking soda, salt and cinnamon. Mix them together with a whisk.
3. In a medium mixing bowl, combine the oil and honey or maple syrup and beat together with a whisk. Add the eggs and beat well, then add the yogurt and vanilla. Mix well. (If the coconut oil solidifies in contact with cold ingredients, gently warm the mixture in the microwave in 30 second bursts.)
4. Pour the wet ingredients into the dry and mix with a big spoon, just until combined (a few lumps are ok). In a small bowl, toss the blueberries with the remaining 1 teaspoon flour (this helps prevent the blueberries from sinking to the bottom). Gently fold the blueberries into the batter. The mixture will be thick, but don’t worry.
5. Divide the batter evenly between the 12 muffin cups (I used an ice cream scoop with a wire level, which worked perfectly). Sprinkle the tops of the muffins with turbinado sugar. Bake the muffins for 16 to 19 minutes, or until the muffins are golden on top and a toothpick inserted into a muffin comes out clean.
6. Place the muffin tin on a cooling rack to cool. You might need to run a butter knife along the outer edge of the muffins to loosen them from the pan. If you have leftover muffins, store them, covered, at room temperature for 2 days, or in the refrigerator for up to 5 days. Freeze leftover muffins for up to 3 months.

Notes

Recipe adapted from my blueberry maple muffins (recipe available in my cookbook) and lemon raspberry muffins.

*Note on Greek yogurt: I’ve used a variety of fat percentages and the muffins have always turned out well. Higher fat yogurt will yield a somewhat more rich muffin. You can also substitute plain (not Greek) yogurt, but your muffins might not rise quite as high.

Make it vegan: You can replace the eggs with flax “eggs.” Replace the yogurt with a smaller amount of vegan buttermilk—just mix ⅔ cup non-dairy milk with 2 teaspoons vinegar. Let it rest for 5 minutes before adding it to the other liquid ingredients. Or, use 1 cup vegan yogurt.

Make it dairy free: See buttermilk option above.

Make it egg free: Substitute flax eggs for the regular eggs.

Make it gluten free: Substitute an all-purpose gluten-free flour blend for the whole wheat flour. Bob’s Red Mill makes a gluten-free blend that works well.

Lemon variation: For lemon blueberry muffins, whisk the zest of 1 medium lemon (about ½ teaspoon), preferably organic, into the liquid ingredients. You could even double that amount for extra-lemony muffins.

Change it up: You can substitute 1 cup of any other muffin-worthy fresh fruit for the blueberries. If you’re using strawberries or other large fruit (like peaches), chop them into small pieces first.

2/18/19 note: I’ve changed the baking temperature from 350 degrees Fahrenheit to 400, and reduced the baking time from 22 to 24 minutes to 16 to 19 minutes. These changes improve the muffin texture (less spongy in the center) and produce more irresistibly golden muffin tops.

Nutrition

The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice. See our full nutrition disclosure here.

• Category: Muffin
• Method: Baked
• Cuisine: American