If you love bright lemon flavors coupled with juicy sweet blueberries, then these healthy Lemon Blueberry Muffins are for you! Sweetened with honey, using whole wheat flour and a little Greek yogurt for a soft, lightly sweet and moist muffin recipe.

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Lemon muffins will always be a forever favorite of mine. The burst of lemon flavor coupled with juicy blueberries in every bite… What more could you want?!
Healthy muffin recipes are also one of my favorite things to bake. They’re quick, easy and make the best snack.
When you add a little lemon glaze, they almost double as a special treat.
Muffin Ingredients
- Bob’s Red Mill Whole Wheat Pastry Flour – the best whole wheat flour with a light and soft texture, perfect for these muffins!
- baking soda & baking powder – use both to get the best rise
- fine sea salt – to enhance flavor
- lemons – You’ll want to grate two medium lemons for lots of lemon zest and flavor. Plus you’ll need 1/4 cup lemon juice.
- yogurt – use a Greek yogurt or Skyr for best results. This muffin recipe was also tested with plant based Skyr and worked wonderfully! For even more flavor, use a lemon flavored yogurt if you can find one!
- honey – I love the golden color and flavor honey adds to these muffins, but maple syrup would likely work as well.
- milk – you can use the milk of your choice such as cow’s, cashew, almond, coconut, etc.
- vanilla extract or lemon extract– You can also substitute almond extract for a delicious different kind of flavor. Though lemon emulsion will give you the most lemon flavor.
- blueberries – you can use fresh or frozen blueberries here. Just note that when using frozen blueberries you’ll need a couple more minutes of bake time.
- poppy seeds – personally I love the added texture but you can also omit if you don’t have them on hand.
Recommended Tools
- 12-cup muffin tin (light metal)

Find the full detailed instructions with measurements in the recipe card below, at the end of this post.
How To Make Blueberry Lemon Muffins
These healthy muffins come together very easily, just like most muffin recipes!
I like to start with mixing together the dry ingredients then setting aside.
Then grab a large bowl and begin adding the wet ingredients – oil, honey, lemon juice, eggs, yogurt, vanilla and milk.
Once all of your wet ingredients are combined, slowly begin add in the flour, fold in the poppy seeds and lemon zest.
Then lastly fold in the blueberries – make sure not to over-mix here or your muffins will be tough and won’t rise as nicely.



Why to Use Yogurt in Muffins
Using yogurt in these blueberry lemon muffins creates a soft, light, fluffy and moist texture! You can use Greek yogurt, Skyr (Icelandic yogurt) or a non-dairy alternative. Just make sure if you’re using a plant based yogurt alternative, it is labeled Greek or Skyr, as it should be thicker than traditional yogurt.

My Best Muffin Baking Tips
Don’t over-mix the batter. It’s okay if some lumps remain at the end. If you mix the flour in too fast and for too long, you’ll end up with dense muffins.
For high muffin tops, bake the muffins first at 425ºF for 5 minutes, then drop the oven temperature down to 350ºF and continue baking for another 10-12 minutes. My muffins were done at 11 minutes, but every oven is different.
Use a cookie scoop to easily dispense the batter into the muffin cups. It’s (almost) mess free and super quick!
For easy clean up, I swear by these specific liners. They haven’t stuck to a single muffin I’ve made yet! (And I’ve made lots!!)

How to Store & Reheat
To freeze, allow the muffins to cool completely and store in an airtight container. Label and enjoy within three months.
To thaw frozen muffins, you can let them come to room temperature or place in fridge overnight. Make sure to enjoy thawed muffins within 2-3 days.
Fresh muffins are best enjoyed within 2-3 days.

Recipe FAQs
Are lemon blueberry muffins healthy?
I like to think these lemon blueberry muffins are on the healthier side because they are naturally sweetened with honey, contain fresh fruits (blueberries!), and we get the extra protein from Greek yogurt.
How many calories in a lemon blueberry muffin?
One blueberry lemon muffin is 177 calories.
How do you make the perfect tall muffin tops?
Start the muffins at a higher oven temperature (425ºF for 5 minutes), then reduce the oven temperature to 350ºF. This lifts the muffin to new heights, resulting in that tall, puffy bakery-style muffin.
How do you keep muffins moist?
The secret ingredient is yogurt! The yogurt adds moisture, fat, and flavor, which makes a super soft and moist muffin that keeps them tasting fresh for days.
More Lemon Dessert Recipes You’ll Love:
If you make this Lemon Blueberry Muffins recipe, be sure to leave a comment and review on the blog! I love hearing from you, and it helps others learn more about the recipe too! Xx Ashley
Lemon Blueberry Muffins
Ingredients
Dry Ingredients
- 1 ¾ cups + 2 tablespoons white whole wheat flour, see notes
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- 1 ½ tablespoons poppy seeds
- ¼ teaspoon fine sea salt
Wet Ingredients
- ½ cup Greek yogurt, or Skyr
- ½ cup honey
- 2 large eggs
- ¼ cup avocado oil or light olive oil
- ¼ cup freshly squeezed lemon juice
- ½ teaspoon lemon emulsion, makes for stronger flavor, can sub vanilla extract
- ¼ cup non-dairy milk
Mix-Ins
- 1 cup fresh or frozen blueberries
- zest of 2 medium lemons
Instructions
- Preheat oven to 425ºF and line 12-cup muffin pan with paper liners.
- Mix dry ingredients: In a medium bowl mix together flour, baking powder, baking soda, poppy seeds, and sea salt.
- Mix wet ingredients: In a large bowl add greek yogurt, honey, eggs, oil, lemon juice, vanilla and milk; whisk until smooth.
- Combine: Gently stir in the dry ingredients into the bowl of wet ingredients. Once almost combined, fold in blueberries and lemon zest. Be careful not to over-mix.
- Distribute in muffin pan: Evenly distribute batter into muffin pan, filling about 3/4 way full. Top with more blueberries if you'd like, for presentation.
- Bake muffins at 425ºF for 5 minutes, then reduce the oven temperature to 350ºF and continue baking another 10-12 minutes, or until inserted toothpick in center of muffin comes out clean. Muffins will be a nice golden color, thanks to the honey.
- Cool: Allow muffins to cool in pan for 5 minutes before transferring to a wire rack to cool completely.
Video
Recipe Notes:
Nutrition Information
This post was originally sponsored by Bob’s Red Mill in 2022. As always, all thoughts and opinions are my own.












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