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Lemon Poppy Seed Muffins

  • Author: Ansley Beutler
  • Prep Time: 15
  • Cook Time: 17
  • Total Time: 32 minutes
  • Yield: 9 Bakery Style Muffins or 12 Standard Muffins 1x
  • Diet: Gluten Free


Say hello to citrus season with these zesty gluten-free lemon poppy seed muffins! They're soft and moist with a little crunch from the tiny poppy seeds. This healthy lemon poppy seed muffin recipe is easy and yes, even better than the Costco famous!



For the muffins

  • 2 eggs
  • 3 Tbsp coconut sugar
  • 1/3 cup honey
  • 1/4 cup almond milk (any nut milk will work)
  • 1/4 cup coconut oil
  • 1 tsp vanilla
  • 3 Tbsp lemon juice (about 1 large lemon)
  • 2/3 cup greek yogurt, plain and fat-free
  • 1 1/2 cup gluten-free oat flour
  • 3 Tbsp coconut flour
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1 Tbsp lemon zest
  • 2 Tbsp poppy seeds, plus extra to top if desired

For the glaze

  • 1 cup organic powdered sugar
  • 1 Tbsp almond milk (any milk will work)
  • 1 Tbsp lemon juice


For the muffins

  1. Preheat oven to 425 F. In a large bowl, whisk the eggs, coconut sugar, honey, almond milk, coconut oil, vanilla, and lemon juice together until well incorporated.
  2. Add in the greek yogurt and mix well to break up the yogurt.
  3. Fold in the oat flour, coconut flour, baking powder, and baking soda. Be careful not to over-mix. Simply fold the batter until no flour clumps remain.
  4. Add the lemon zest and poppy seeds to the batter and fold to distribute. Again, be careful not to over-mix.
  5. Pour the batter into the muffin liners (see notes below on liner options). Fill the liner up almost to the top, leaving only about 1/2 inch at the top of the liner.
  6. Bake in the oven for 7 minutes. Leaving the muffins in the oven, reduce the heat to 350 and bake for another 10 - 12 minutes until the tops of the muffins begin to turn a yellow-ish gold.
  7. Allow the muffins to cool before drizzling with the glaze.

For the glaze

  1. In a small bowl, stir together the powdered sugar, almond milk, and lemon juice until the powdered sugar is well mixed. The glaze should be slightly thick. If it's too runny, add another Tbsp of powdered sugar until you reach the desired consistency. If it's too thick, add another Tbsp of almond milk.
  2. Drizzle the glaze over each of the cooled muffins. Sprinkle a few extra poppy seeds over top if desired and enjoy!


Greek yogurt substitutions : Any fat-free or low-fat yogurt will work in this gluten-free lemon poppy seed muffin recipe. A dairy-free yogurt like coconut yogurt will work as well. Just make sure the yogurt is unsweetened.

Almond milk substitutions : Any nut milk or dairy-free milk will work in this recipe. I recommend unsweetened almond milk or oat milk.

Glaze options : If desires, you can easily substitute the powdered sugar glaze with melted coconut butter. Add about a teaspoon of lemon juice to the melted coconut butter to provide a touch of citrus flavor!

Muffin Liners : You have three options for the muffin liners:

  • Traditional muffin liners - This is the easiest option. You can usually find muffin liners at your local grocery store.
  • No muffin liners - If you choose this option, make sure to grease each of the muffin molds well with coconut oil or butter. You will also want to make sure the muffins are completely cool before running a knife around the edge to lift them out of the pan.
  • Home made muffin liners - This is the most fun option in my opinion! Homemade muffin liners are easy to make too. Simply cut 5 X 5 squares out of parchment paper. You don't have to be exact with it, it's actually more fun it they aren't all the same size! Press each square into the muffin tin with the bottom of a glass. Any small bottle will work for this. I'm sure if you look in your pantry you'll find one - think ketchup bottles or salad dressing bottles! And that's it!

Storing :

These gluten-free lemon poppy seed muffins are best stored in an airtight container. They will keep for up to 5 days on the counter and a week in the fridge. Keep in mind, if you use a powdered sugar style icing, it will soak into the muffin if muffins are in a slightly warm environment (aka next to the stove or toaster). This is fine! Your muffins will still taste the same. Just know that the icing is still on the muffins, it's just melted into it (umm YUM).

  • Category: Muffins
  • Method: Bake
  • Cuisine: American

Keywords: gluten-free lemon poppy seed muffins, healthy lemon poppy seed muffins, gluten-free muffins