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These healthy lemon poppy seed muffins are a lighter twist on the classic recipe. These soft and moist muffins are bursting with lemon flavor and covered in a lemon icing.

Healthier lemon poppy seed muffins iced on a counter
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I grew up on lemon poppy seed muffins and they have a nostalgic place in my hear. These healthier lemon poppy seed muffins are made with lighter ingredients like coocnut oil, oat flour, and greek yogurt. They’re also gluten-free!

Why You’ll Love These Healthy Lemon Poppyseed Muffins

  • Easy to make
  • Tons of lemon flavor
  • Just like the bakery classic
  • Made with healthier ingredients
  • Gluten-free
Healthier lemon poppy seed muffins batter in a glass bowl with a whisk in it

Ingredients You Need

Here are the ingredients to make these lemon poppy seed muffins. Skip to the recipe card for exact measurements.

  • Oat flour: the base and structure of the muffin. Buy it from the store or make your own oat flour.
  • Tapioca flour: the combination of these two flours make a delicious healthy muffin base.
  • Sugar: just a little to sweeten these. Honey is a great alternative.
  • Baking powder and soda: to help the muffins rise.
  • Salt, almond extract, and vanilla extract: for flavor.
  • Poppy seeds: for the signature lemon poppy seed flavor.
  • Coconut oil: refined coconut oil is best for less coconut flavor.
  • Greek yogurt: for protein and a tender crumb.
  • Eggs: to bind the batter. Room temperature is best!
  • Milk: to think out the batter.
  • Lemons: use the juice from 1 lemon and zest from 2 lemons.
Healthier lemon poppy seed muffins batter in muffin tin with paper cups

How to Make Healthy Lemon Poppy Seed Muffins

Here are the steps to make these easy lemon poppyseed muffins. Skip to the recipe card for the printable recipe.

  1. Dry ingredients: Mix the dry ingredients, including the poppy seeds, in a mixing bowl.
  2. Wet ingredients: whisk all of the wet ingredients in a separate bowl.
  3. Combine the batter: add the dry ingredients to the wet ingredients and fold to combine. Don’t over mix.
  4. Let the batter rest: Cover the bowl and rest at room temperature for at least 20 minutes, or up to an hour. You can also refrigerate overnight.
  5. Fill muffin tins: line a muffin tin with 12 paper liners or in every other tin with 6 liners and bake them in two batches (I prefer this for taller muffins). Fill the muffin tins all the way full.
  6. Bake: Bake the muffins at 425 for 7 minutes then reduce the heat to 350 and continue baking for 8-10 minutes. Be sure to set the temp back to 425 if you’re baking in 2 batches.
  7. Glaze: whisk the glaze ingredients together and drizzle it over the muffins.
bag of icing being squeezed onto healthier lemon poppy seed muffins

Tips for the Best Lemon Poppy Seed Muffins

  • Use room temperature ingredients.
  • Let the muffin batter rest to start activating the baking powder before it bakes.
  • Bake the muffins in two two batches to separate them in the muffin tins. It helps them rise with tall domes.
  • Don’t skip the glaze!
Healthier lemon poppy seed muffins stacked in a carton on a counter with more muffins surrounding it
Glazed healthier lemon poppy seed muffins on a cutting board with lemon slices
Healthier lemon poppy seed muffins cut in half with the inside of the halves facing upward on a counter top

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4.28 from 11 votes

Healthy Lemon Poppy Seed Muffins

Prep: 15 minutes
Cook: 15 minutes
Total: 30 minutes

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Servings: 12

Ingredients

  • 1 1/2 cups oat flour
  • 1/2 cup tapioca flour
  • 1/2 cup cane sugar
  • 2 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 2 Tablespoons poppy seeds
  • 1/2 cup refined coconut oil melted
  • 2/3 cup plain Greek yogurt
  • 2 large eggs room temperature
  • 3/4 cup milk room temperature
  • 2 Tablespoons lemon zest (about 2 lemons)
  • 2 Tablespoons lemon juice (about 1 lemon)
  • 1 teaspoon vanilla extract
  • 1/4 teaspoon almond extract

Lemon Glaze and Icing

  • Juice from 1 lemon divided
  • 1/2 cup powdered sugar
  • 1/4 cup Greek yogurt

Instructions 

  • In a large bowl, whisk together the oat flour, tapioca flour, sugar, baking powder, baking soda, salt, and poppy seeds.
  • In another medium bowl, whisk together the melted coconut oil, eggs, sour cream, vanilla extract, almond extract, lemon zest, lemon juice, and milk.
  • Pour the wet mixture into the dry ingredients and use a rubber spatula to combine. Do not over mix.
  • Cover the bowl with plastic wrap or a towel and rest at room temperature for at least 20 minutes, or up to an hour. You can also place in the fridge overnight.
  • While it's resting, preheat the oven to 425°F. Line a muffin tin with one of these two options: 1) line with 12 paper liners or 2) line every other muffin tin with 6 paper liners and bake in 2 batches, which gives you taller muffin tops (I prefer option 2).
  • Use a large (2 oz) cookie scoop, or about 1/4 cup) to scoop the muffin batter into the prepared muffin tin. Be careful not to deflate the batter.
  • Bake for 8 minutes in the preheated oven then reduce the oven temperature to 350°F and continue to bake for 8-10 minutes. Be sure to set the temp back to 425 if you're baking in 2 batches.
  • Let them cool for 5 minutes in the pan then transfer the muffins to a cooling rack to cool another 20 minutes. While they're cooling, make the glaze. Whisk together the lemon juice, powdered sugar, and Greek yogurt. Drizzle on top of the muffins and serve.
Last step! If you make this, please leave a review letting us know how it was!
4.28 from 11 votes (11 ratings without comment)

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1 Comment

  1. WholeYum says:

    These lemon poppyseed muffins looks so good! We would love to see the recipe on WholeYum!