Sweet and juicy blueberries and tart lemon are the perfect flavor combination for these healthy blueberry lemon protein muffins. Light, fluffy, and have 10 grams of protein per serving.

Want this recipe sent to you?
This post may contain paid links. If you click on a link and make a purchase, I may receive a small commission at no extra cost to you. For more information, please read my disclaimer.
Why You'll Love These Gluten-Free Lemon Blueberry Muffins
- Healthy muffins that make a great sweet breakfast or snack. Blueberries are a great source of
- Use fresh or frozen berries. Blueberry lemon muffins use fresh or frozen blueberries.
- Extra protein. Made with Greek yogurt and vanilla protein powder for extra protein (just like this chocolate chip protein muffin).
- Great flavor. Delicious lemony muffin bursting with lemon flavor!
- Use up lots of blueberries. Great way to use up extra blueberries in the summer(just like our Kodiak Cakes blueberry muffin).
- Delicious texture! Fluffy muffins with a light texture.
- Gluten-free and can be made dairy-free.
Ingredients and Substitutions
Here are the ingredients you need to make this recipe. Reference the recipe card at the bottom for exact measurements and the notes below for substitution ideas.

Dry Ingredients
- Gluten-free baking flour or all-purpose flour works best in this recipe. I have not substituted almond flour, whole wheat flour, oat flour, or coconut flour.
- Protein powder: Use either a vegan protein powder or whey protein, whichever works for your preference.
- Salt and Baking powder: Used to give the blueberry lemon protein muffins a light and fluffy texture.
Wet Ingredients
- Cane sugar sweetens the muffins. Use coconut sugar, brown sugar, maple syrup, honey, or monk fruit sweetener as an alternative.
- Plain Greek yogurt or vanilla Greek yogurt helps to add more yogurt and give a moist texture. Sour cream is a good substitute.
- Coconut oil is the fat source in the muffin. Use butter or vegetable oil as an alternative.
- Fresh Lemons: Fresh lemon juice and lemon zest provide a tangy and fresh flavor.
- Fresh blueberries, wild blueberries, or frozen blueberries all work well in this blueberry lemon protein muffin.
- Vanilla Almond milk: Adds additional moisture if needed. Use dairy milk if you wish.
- Large eggs: Provide binding and help to create texture. I have not tested a flax egg.
- Lemon extract (not shown) bumps up the lemon flavor. Vanilla extract works as a substitute or omit if you do not have it on hand.
How to Make Lemon Blueberry Protein Muffins
Below are step-by-step instructions for how to cook this recipe with the best results. The recipe card at the bottom shows the exact cooking time and temperatures.

- Preheat the oven to 425°F and line a muffin pan or muffin tin with muffin liners. Spray the muffin cups with cooking spray. Use a measuring cup to measure out the dry ingredients and add them to a large bowl.
- In a separate large mixing bowl, stir the wet ingredients together until smooth.
- Add dry ingredients to wet ingredients and fold in blueberries. Mash half of the blueberries with a fork before adding
- Use a cookie scoop or ice cream scooper to scoop the muffin batter into paper liners and measure out 10-12 large muffins, depending on the size of your scoop.
Recipe Variations
- Different fruit. Try different fresh or frozen berries. Raspberries and strawberries both work as substitutes for blueberries in this recipe.
- Dairy-free. Make dairy-free lemon blueberry muffins by swapping Greek yogurt for nondairy yogurt.
- Sweet topping. Add some powdered sugar to the top of the muffins for some extra sweetness.
Expert Tips
- For best results, follow the recipe card as written.
- Allow blueberry lemon protein muffins to cool to room temperature on a cooling rack before storing.
What to Serve with Lemon Blueberry Muffins
Serving them with a serving of Greek yogurt is an easy breakfast for kids, teens, or adults, just like our blueberry muffins with protein.
Add these easy muffins to a holiday brunch (they are great for Easter brunch!) or with a side of scrambled eggs and fresh fruit.
Make Ahead
Blueberry lemon protein muffins are one of my favorite easy breakfasts to make ahead.
I usually make a batch to eat for at least five days of breakfasts or easy snacks.
Storing Leftovers
Store leftover muffins in a sealed or airtight container at room temperature for 3-4 days. Refrigerate for longer storage.
Freezing
Store lemon blueberry protein muffins in the freezer in a freezer bag for up to 3 months.
Recipe FAQs
If you do not have baking powder on hand, substitute baking soda by using ¼ teaspoon for each teaspoon of baking powder. Also, add ½ of a teaspoon of lemon juice or white vinegar.
Yes! According to Healthline, blueberries are a healthy fruit. Adding them to this lemon blueberry protein muffin makes them even better.
Low-carb lemon blueberry bars are one of my favorite easy summer desserts to make with lemon flavor and fresh blueberries.

Other Healthy Muffin Recipes to Try
If you've made this recipe, would you please leave a star rating and comment below on the recipe card? If you want more simple + delicious eats, please subscribe to my newsletter and follow along on Facebook, Pinterest, and Instagram for the latest updates.
Healthy Blueberry Lemon Protein Muffins
Ingredients
Wet Ingredients
- ½ cup coconut oil softened
- 2 whole eggs
- ½ cup almond milk add slowly if needed
- ⅓ cup Greek yogurt plain or vanilla
- 1 teaspoon lemon extract
- 1 whole lemon juice and zest
- 1 cup cane sugar
Dry Ingredients
- ½ cup vanilla protein powder
- 2 cups gluten-free flour
- ½ teaspoon salt
- 2 teaspoon baking powder
Other Ingredients
- 2 cups fresh blueberries
Instructions
- Start by preheating your oven to 425F and creaming the coconut oil and sugar.½ cup coconut oil, 1 cup cane sugar
- Once the coconut oil and sugar mixture is creamy, add eggs, one at a time, beating well after each addition. Then, add the lemon extract, Greek yogurt, lemon juice, and lemon zest.2 whole eggs, 1 teaspoon lemon extract, 1 whole lemon
- Sift and/or whisk together the flour, protein powder, salt, and baking powder. Then, add to the wet ingredients alternatively with the almond milk.½ cup almond milk, ½ cup vanilla protein powder, 2 cups gluten-free flour, ½ teaspoon salt, 2 teaspoon baking powder, ⅓ cup Greek yogurt
- Crush half of the fresh blueberries with a fork and mix into the batter. Fold in the remaining blueberries.2 cups fresh blueberries
- Line a muffin tin with silicone liners or muffin liners sprayed with coconut oil spray and fill with batter using an ice cream scoop.
- Bake at 425F for 5 minutes. Lower heat to 350F and bake for 15-20 minutes. Check muffins for doneness by inserting a toothpick in the center and when it comes out clean, they are done.











Taylor says
These were delicious 10/10
Lyndsey Piccolino says
Thanks Taylor! I'm so glad you liked them.
Nichole says
The flavor was great , but they were too heavy. Mine didn’t rise very much either. If I baked again I think I would leave out the protein powder. I think that may have made them heavy.
Lyndsey Piccolino says
Thanks for trying the recipe Nichole! Different protein powders would definitely have different effects. I usually use Orgain Vanilla and have no issues.