Lemon Blueberry Muffins

lemon blueberry muffin in its wrapper on parchment paper setting on cooling rack, surrounded by other baked muffins, blueberries and lemon wedges

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

4.3 from 6 reviews

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.



Dry Ingredients

  • 1.75 cups + 2 tablespoons whole wheat pastry flour
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1.5 tablespoons poppy seeds
  • 1/4 teaspoon fine sea salt

Wet Ingredients

  • 1/4 cup freshly squeezed lemon juice
  • 1/2 cup of Greek yogurt or Skyr
  • 2 large eggs
  • 1/4 cup avocado oil or light olive oil
  • 1/2 teaspoon vanilla extract
  • 1/2 cup honey
  • 1/4 cup non-dairy milk
  • zest of 2 medium lemons
  • 1 cup fresh or frozen blueberries


  1. Preheat oven to 425ºF and line 12-cup muffin pan with paper liners (I love these ones – no sticking!)
  2. Mix dry ingredients: In a medium bowl mix together flour, baking powder, baking soda, poppy seeds, and sea salt.
  3. Mix wet ingredients: In a large bowl whisk together 
  4. 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.
  5. 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.
  6. 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.
  7. Cool: Allow muffins to cool in pan for 5 minutes before transferring to a wire rack to cool completely.


To make dairy-free, use a thick plant based Greek yogurt or Skyr. These were tested with Siggi’s plant based.

This recipe has not been tested with flaxseed eggs yet or gluten-free flour, but let me know if you try! Using Bob’s Red Mill 1:1 Gluten-Free Baking Flour is your best gluten-free flour substitute for this recipe. I would not recommend replacing both the flour and the eggs.