Whole Wheat Blueberry Muffins
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These whole wheat blueberry muffins are muffin PERFECTION. And they are 100% whole wheat, although you would never know it. There’s a few secrets to getting these tender, fluffy muffins that I’ll share with you in the post!

These whole wheat blueberry muffins are bursting with fresh, juicy blueberries and made with 100% whole wheat flour. The best part about homemade muffins is that they take about 10 minutes to prepare.
I feel like when whole wheat sometimes get a bad rep. When you hear whole wheat you might think you are giving up on flavor for more nutrition. But I promise you that these muffins are anything of the sort. These muffins are a healthier version on the Boston Jordan Marsh department store blueberry muffins. Now I can’t say I’ve ever had an original, but from what I hear they’re awesome on their own. So I figured why not make a whole wheat version?
Yes I promise you these are just as amazing as their white flour cousins. And if you’re like me you are finding all sorts of way to put those fresh summer berries into whatever you can find. So why not a delicious, whole wheat muffin? I know what you’re thinking…what a great idea! I think so too.😆
I actually make whole wheat blueberry muffins with my Home Ec students to show them that using whole wheat flour still equals = awesomeness. The fact that they scarf them down tells me they agree.
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Ingredients Needed

Ingredient Notes
- Whole Wheat Flour – I used white whole wheat flour, which yields a softer texture than regular 100% whole wheat flour as it’s a different variety of wheat. But you can use traditional 100% whole wheat flour, but you want to replace by weight, so you would need to use 2 cups whole wheat flour.
- Milk – You can use really any kind of milk- whole, low-fat, or another plant-based milk such as soy or almond milk.
- Blueberries – I used fresh blueberries, but frozen blueberries can also be used. You will mash half of the berries before adding them to the batter, but ONLY if they are fresh. If using frozen, do not thaw them first, as will create too much moisture. Simply rinse them a few times, and be sure to not smash them while you stir them in.

How To Make These Whole Wheat Blueberry Muffins
- Cream the butter and sugar. In a medium-sized bowl, beat together the butter and sugar until well combined.
- Add eggs. Add the eggs one at a time, scraping the sides and bottom of the bowl and beating well after each addition.Beat in the baking powder, salt, and vanilla.
- and 4. Add flour and milk. Add the flour alternately with the milk, beating gently just to combine. Scrape the bottom and sides of the bowl.

Baking 101: Measure your flour correctly. Measuring your flour wrong is one reason why homemade muffins don’t come out fluffy and moist like they do as a bakery. The best way is to use a scale and measure by weight. If you do use your measuring cups, then be sure to first fluff up the flour. Then scoop with a spoon into the cup and then level off with a flat edge. For more on how and why to measure your flour you can read this post.
- Mash blueberries. Mash 1/2 cup of the blueberries.
- Add blueberries. Add the mashed and whole berries to the batter, stirring just to combine and distribute.
- Scoop batter. Scoop the batter by the heaping 1/4-cupful into the prepared muffin pan; a muffin scoop works well here.
- Sprinkle on sugar. Sprinkle about 1 teaspoon granulated sugar atop each muffin. Bake the muffins for about 30 minutes, until they’re light golden brown on top, and a toothpick inserted into the middle of one of the center muffins comes out clean. Remove the muffins from the oven, loosen their edges from the pan, and after about 5 minutes transfer them to a rack to cool.

Tips and Tricks
- Do not overmix. You want to make sure to mix just until the flour is mixed in. If you keep mixing, then you activate the gluten protein in the flour which can make your muffins tough and chewy. And cause “tunneling” which are these long holes throughout your muffins. So. Do. Not. Overmix. Ok? Ok.
- Test for doneness. It can be tough to tell if your muffins are done. I like to use a toothpick inserted into a muffin in the middle of the tin and look for moist crumbs clinging to the toothpick. If you see batter still then pop them into the oven for a few minutes.
- Cool In Muffin Tin For 5 Minutes. Once you have taken your muffins out of the oven you want to let them cool for about 5 minutes in tin. If you try to take them out right away, I find they tend to fall apart and need a few minutes to cool to set up. After the 5 minutes, then move them from a tin to a cooling rack. If you leave the muffins in the tin, then the heat from the tin will cause them to continue to bake possibly causing them to overbake.

Recipe FAQ’s
These muffins will be good covered at room temperature for a few days, or in the refrigerator up to 1 week.
You can freeze baked muffins once they are cooled for up to 3 months. You can just thaw at room temperature before serving.
Yes you can, the baking time should be around 9-11 minutes.

More Recipes To Try
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Whole Wheat Blueberry Muffins
Ingredients
- 1/2 cup (1 stick, 113 g) unsalted butter at room temperature
- 1 cup (200 g) granulated sugar
- 2 large eggs room temperature
- 2 teaspoons baking powder
- ½ teaspoon salt
- 1 ½ teaspoons vanilla extract
- 2 cups + 2 Tablespoons (240 g) White whole wheat flour
- ½ cup (113 g) milk
- 2 ½ cups (354 g) blueberries fresh or frozen*
- ¼ cup (50 g) sugar for topping
Instructions
- Preheat the oven to 375°F. Lightly grease a standard 12-cup muffin tin; or line the tin with papers, and grease the papers.
- In a medium-sized bowl, with an electric mixer cream together the butter and sugar until light and fluffy, about 2 minutes.
- Add the eggs one at a time, scraping the sides and bottom of the bowl and beating well after each addition.
- Beat in the baking powder, salt, and vanilla.
- Add the flour alternately with the milk, beating gently just to combine. Scrape the bottom and sides of the bowl as needed.
- Mash 1/2 cup of the blueberries. Add the mashed and whole berries to the batter, stirring just to combine and distribute. Do not overmix. If using frozen berries, do not mash any of them but add them all right to the batter.
- Scoop the batter by the heaping 1/4-cupful into the prepared muffin pan; a muffin scoop works well here.
- Sprinkle about 1 teaspoon granulated sugar atop each muffin.
- Bake the muffins for about 30 minutes, until they’re light golden brown on top, and a toothpick inserted into the middle of one of the center muffins comes out clean.
- Remove the muffins from the oven, loosen their edges from the pan, and after about 5 minutes transfer them to a rack to cool.
Notes
- Storage: These muffins will be good covered at room temperature for a few days, or in the refrigerator up to 1 week.
- Freeze: Freeze cooled, baked muffins for up to 3 months, wrapped well. Thaw, uncovered, at room temperature.
- Whole Wheat Flour – I used white whole wheat flour, which yields a softer texture than regular 100% whole wheat flour as it’s a different variety of wheat. But you can use traditional 100% whole wheat flour, but you want to replace by weight, so you would need to use 2 cups whole wheat flour.
- Milk – You can use really any kind of milk- whole, low-fat, or another plant-based milk such as soy or almond.
- Blueberries – I used fresh blueberries, but frozen blueberries can also be used. If using frozen, do not thaw them first, as will create too much moisture. Simply rinse them a few times, and be sure to not smash them while you stir them in.
- Mini muffins: Yes you can bake these into mini muffins, but the baking time should be around 9-11 minutes.

I made this a couple days ago and they were really good! Followed the recipe exactly and they turned out great! Also gives me a little less guilt using whole wheat flour!?
So happy you enjoyed them! Whole wheat flour is our little secret for keeping these muffins wholesome without sacrificing flavor. Thanks for baking along—hope you bake them again soon! 😊
These just came out of the oven, so I haven’t tried one yet, but I already know that they’ll be the best I’ve ever made/eaten! I used coconut sugar in the batter but still used granulated on top. Also, I followed the recipe to a T! And didn’t over mix, because that’s crucial. Perfect baking time as well. 🙂 thank you for the awesome recipe because I’ve been botching my baking lately (stress) and I needed the win today.
Your comment just made my day! 🥹💙 So thrilled they turned out perfectly for you—and LOVE the coconut sugar tweak! Baking wins are the best stress-relievers. Enjoy every bite (and pat yourself on the back for nailing it!). Thanks for sharing your joy with me! 🫐✨