Whole Wheat Blueberry Muffins
These whole wheat blueberry muffins are everything you want in a healthy baked good — soft, fluffy, and full of flavor with just the right amount of sweetness. They’re made with nutrient-dense ingredients, but the texture is so moist and tender that no one will know they’re 100% whole wheat.
Whether you enjoy them as part of a healthy breakfast or nutritious snack, this is a recipe you’ll want to make on repeat.
If you want more healthy muffin recipes, they’re kind of my thing. Try my Instagram-viral protein blueberry muffins, healthy honey bran muffins, or easy blender banana muffins.
Why you’ll love this dietitian-made recipe
- High in fiber: Whole wheat flour adds three-times more fiber than all-purpose, helping you stay full and satisfied. For more high-fiber foods, check out this printable list of the top fiber-rich foods.
- Naturally sweetened: These muffins use honey for sweetness and a little extra nutrition in every bite.
- Moist and crave-worthy: Forget dry, dense whole wheat muffins — these are soft, fluffy, and perfectly sweet.
Nutrition highlight — what makes these muffins healthy
As a balanced Registered Dietitian, I love these whole wheat blueberry muffins because they’re packed with nutrition but still taste like a treat. Blueberries add antioxidants, Greek yogurt boosts the protein (try more healthy recipes with Greek yogurt), and whole wheat flour brings extra fiber and minerals to every bite.
Key ingredients and swaps
- Butter: I love the flavor that butter adds, but you can swap it for canola or vegetable oil if you prefer. Olive oil also works well, though it brings a slightly more savory flavor.
- Plain Greek yogurt: I recommend low-fat plain Greek yogurt (I usually use 2%). This recipe hasn’t been tested with dairy-free yogurt, so I don’t suggest making that swap.
- Milk: I use 2% dairy milk because that’s what I keep on hand, but any milk or milk alternative should work here.
- Honey: These muffins are naturally sweetened with honey, but you could use another liquid sweetener like maple syrup or agave if needed.
- Lemon: The zest and juice add brightness and balance while helping the muffins rise. Don’t skip it—it makes a big difference!
- Blueberries: Fresh or frozen both work. If you’re using frozen, add them straight from the freezer—no need to thaw.
Scroll down to the recipe card for the full ingredients list and detailed recipe.
How to make whole wheat blueberry muffins
Step 1: Whisk wet ingredients together.
Step 2: Whisk dry ingredients and toss in blueberries, then add wet ingredients.
Step 3: Gently mix until just combined.
Step 4: Transfer to prepared muffin pan and bake.
Ever wonder why we toss the blueberries in flour before mixing with the wet ingredients? This prevents the blueberries from sinking to the bottom of the muffins!
Top tips for success
- Do not over-measure your flour. Too much flour makes for dry and tough muffins. Make sure to use the spoon and level method when measuring.
- Don’t over-mix the batter. Whole wheat muffins can easily become tough and dense if you mix the batter for too long. Gently mix until just combined — it’s okay if you see some clumps of flour.
- If you’re using frozen blueberries, work fast. Use them straight from the freezer and don’t let them defrost. They’ll start releasing liquid as they reach room temperature, and can mess with the color and texture of your muffins.
Common questions
Yes, the batter for these whole wheat blueberry muffins comes together quick and is very thick. Totally normal!
Yes, you can use fresh or frozen blueberries in this muffin recipe. If you’re using frozen, make sure to use them right from the freezer and don’t let them de-frost. Once they start coming up to room temperature, they’ll release liquid — this can change the color of the batter and texture of the muffins.
Whole wheat blueberry muffins will last for up to three days at room temperature. But I recommend letting them cool to room temperature and keeping them covered in a food container or sealed bag.
You can freeze these muffins for up to three months, but the fridge will dry them out. To freeze, let the muffins completely cool to room temperature and store in a sealed freezer-safe bag or container. De-frost on the counter overnight, or gently warm from frozen in the microwave.
More healthy muffin recipes
Brownie Black Bean Muffins
Honey Bran Muffins
Chocolate Chip Protein Muffins
Apple Cinnamon Oat Muffins
Blender Banana Muffins
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Whole Wheat Blueberry Muffins
Ingredients
Wet Ingredients
- ½ cup butter, melted and cooled
- 1 cup plain Greek yogurt, I used 2% fat
- ½ cup honey
- ¼ cup milk
- 2 tsp vanilla extract
- 2 large eggs
- lemon zest, from 1/2 a lemon
- 1 Tbsp lemon juice
Dry Ingredients
- 2 cups whole wheat flour, spooned and levelled
- 1 tsp baking powder
- ¾ tsp salt
- ½ tsp baking soda
- ½ tsp cinnamon
- 1 cup blueberries, plus more for sprinkling on top
Equipment
- 3-Tbsp cookie scoop optional
Instructions
- Position oven rack to the middle and pre-heat to 350 F. Line your muffin pan with liners and set aside.
- To a large mixing bowl, add all wet ingredients. Whisk until smooth and set aside.
- To a separate large mixing bowl, add all dry ingredients except blueberries. Whisk together until combined. Then, add blueberries and gently toss to coat in flour.
- Add dry ingredients to wet ingredients. Use a wooden spoon or spatula to gently mix until just combined. Don't over-mix or your muffins will be dry and tough — it's okay if there's a few clumps of flour remaining.
- Spoon batter into prepared muffin pan. I like to use a cookie scoop for this step to make it easy, but you can use what you have. Each muffin liner will be filled to the top. Press 3-4 blueberries on top of each muffin if desired.
- Bake for 22-27 minutes, or until lightly golden and set, and a toothpick inserted into the center comes out mostly clean with just a few moist crumbs.
- Let the muffins rest in the pan for 5-minutes before transferring to a wire rack. Let them cool for an additional 15-minutes before eating. Enjoy!
Notes
- Liners: Paper liners will work, but I like silicone better to prevent any sticking.
- Blueberries: If using frozen blueberries, use them right from the freezer and don’t let them de-frost.
- Timing: These muffins always take exactly 25 minutes in my oven.
- Important notes: Don’t over-measure flour, and don’t over-mix your batter. This is key to preventing dry and tough muffins.
My sister helped me taste test these and she agreed they don’t taste whole wheat, and they have the perfect hint of lemon. You will love them!