Gluten-Free Lemon Poppyseed Muffins


These gluten-free lemon poppyseed muffins are made with almond and coconut flour and have a bright, lemony flavor. You can top the muffins with the lemon glaze for a real treat or leave it off.

I’ve always been a fan of lemon treats. They’re decadent, yet light and refreshing and perfect for spring. The crazy thing is that I didn’t have any sweet lemon recipes here on EBF… until now! So these lemon poppyseed muffins are the first and let me tell ya, they were worth the wait. They’re so tasty, come together in no time and can be eaten for breakfast, snack or dessert.

Plate piled with lemon poppyseed muffins topped with a glaze and lemon zest.

I rarely get confused with the difference between muffins and cupcakes, but these kind of have me stumped! They are light, fluffy and decadent like a cupcake but the healthy ingredients have me leading toward muffin. Since I doubt you’d eat these for breakfast if I called them a cupcake, I decided to go with muffin. Ha! What do you think?!

Stack of three lemon poppyseed muffins with a glaze. The top muffin has a bite taken out of it.

Here’s What You Need

  • eggs 
  • coconut sugar
  • coconut oil
  • lemon juice & lemon zest
  • almond and coconut flour 
  • baking powder
  • poppy seeds 
  • lemon glaze – an optional, but highly recommended topping! The glaze takes these to the next level.
Lemon poppyseed muffins on a plate. One has a bite taken out of it.

Why Room Temperature?

As you may have noticed, I specifically noted that a few ingredients for this muffin recipe need to be room temperature! If your eggs and lemon juice are cold, the coconut oil will solidify and create clumps and it’s hard to mix. If this happens, you can set the bowl in a larger bowl of hot water until the coconut oil melts or put it on the stove-top as your oven preheats. Be careful that the mixture doesn’t get too hot or the eggs will cook. Ah baking… a balancing act. 😉

This is how your batter should look. All mixed together without little clumps of coconut oil.

Mixing bowl with lemon poppyseed muffin batter.

Baking with Gluten-Free Flour

I actually shared an entire blog all about using different types of flours. The truth is, there isn’t one gluten-free flour that works best for all recipes and you can’t just swap in the same amount of an alternative flour for all-purpose flour. If you have the patience to experiment, go for it! Otherwise lean on already developed and tested recipes like this one that are sure to turn out correctly!

Two side by side photos of lemon poppyseed muffins in a muffin tin and a close up a muffin.

Storage Tips

While these muffins would be perfect for Easter or Mother’s Day brunch, they don’t have to be for a fancy occasion! I may or may not have already made this recipe a few times this spring, just to have as a treat.

If you’re making these ahead of time and plan to enjoy all week long, I have a few tips for you!

  1. First, let them cool completely. I can’t stress this enough. Let your baked goods cool completely on a wire rack before putting in a storage container. If you skip this step, the heat creates condensation/moisture and you’ll end up with soggy muffins. Not exactly what we want!
  2. My second tip is to keep the glaze separate. You can still prep it in advance if you want, but store it in a separate container. When you’re ready to enjoy, glaze away!
  3. Last but not least because the muffins and glaze don’t have preservatives, I recommend storing them in the fridge rather than on your counter top. They’ll last longer and they taste delicious straight from the fridge.
Plate with lemon poppyseed muffins topped with lemon zest and a glaze.

Try These Muffin Recipes

Be sure to check out all of my muffin recipes on EBF!

Lemon Poppyseed Muffins

5 from 39 votes
These gluten-free lemon poppyseed muffins are made with almond and coconut flour and have a bright, lemony flavor. You can top the muffins with the lemon glaze for a real treat or leave it off.
Plate with lemon poppyseed muffins topped with lemon zest and a glaze.
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Servings 12


  • 5 eggs, at room temp
  • ¾ cup coconut sugar
  • ½ cup coconut oil, liquid state/melted
  • ¼ cup lemon juice, at room temp
  • ½ Tablespoon lemon zest
  • 2 cups almond flour
  • ¼ cup coconut flour
  • 1 Tablespoon baking powder
  • 2 Tablespoons poppy seeds
  • lemon glaze, optional

Lemon Glaze 

  • ½ cup powdered sugar
  • 1 Tablespoon lemon juice


  • Preheat oven to 350°F. Place 12 paper or silicone liners in your muffin tin. 
  • In a medium bowl, mix together eggs, coconut sugar, coconut oil, lemon juice and lemon zest with a whisk. I made a note to make sure your eggs and lemon juice are at room temperature otherwise the coconut oil will solidify and create clumps. If this does happen, you can set the mixing bowl on the warm part of your oven as it’s preheating or set the bowl in a larger bowl of hot water until the coconut oil melts again. Just be sure you don’t get it too hot or else the eggs will start cooking. 
  • In another mixing bowl, whisk together the almond flour, coconut flour, baking powder and poppy seeds. Pour the liquid mixture into the bowl with the dry and stir until mixture is fully combined without any lumps. 
  • Pour the batter evenly into the prepared muffin tin, filling each cavity about ⅔ of the way full. Bake for 23-25 minutes or until a toothpick inserted in the center of the muffin comes out clean.
  • Let muffins cool in the tin for about 10 minutes or so, then remove and let cool completely on a wire rack. 
  • To make the lemon glaze, whisk together the powdered sugar with lemon juice until no lumps remain. If the glaze is too thick, add a little more lemon juice. If the glaze is too thin, add a little more powered sugar.
  • Drizzle glaze over each muffin just before serving. 
  • Store muffins and glaze in separate storage containers in the fridge for up to 5 days. 



  • Recipe inspired and adapted from this Keto Lemon Cake.
  • I haven’t tested this recipe with an egg replacement and I’m not certain it would work well with flaxseed eggs. You’re welcome to test it but the results might not be ideal.


Serving: 1muffin (without glaze) Calories: 291kcal Carbohydrates: 28g Protein: 7g Fat: 21g Saturated Fat: 9g Polyunsaturated Fat: 2g Cholesterol: 77mg Sodium: 163mg Fiber: 3g Sugar: 16g
Course: Breakfast
Cuisine: American
Keyword: lemon poppyseed muffins


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Recipe Rating

    1. Holly
      April 14, 2022 AT 3:39 pm

      5 stars
      I have half a can of poppyseed filling to use up. Made these delicious muffins and the only problem is I can’t stop eating them. Yum.

      1. Brittany Mullins
        April 15, 2022 AT 8:01 am

        I know that problem often, Holly 🙂 So glad you’re enjoying these muffins, thanks for making them and leaving a review!

    2. Trova Yeaman
      April 4, 2022 AT 1:39 pm

      4 stars
      Very tasty! Almost too much poppy seeds…. But still very good!

      1. Brittany Mullins
        April 5, 2022 AT 8:26 am

        Glad you liked these muffins, Trova! I appreciate your review 🙂

    3. Rosemarie
      February 18, 2022 AT 8:42 pm

      Do you think Bob’s Red Mills Gluten-free flour be used instead if the almond and coconut flour?

      1. Brittany Mullins
        February 20, 2022 AT 1:31 pm

        Hi, Rosemarie. I don’t recommend substituting the coconut flour, as it soaks up more liquid than other flours and you cannot swap it 1:1.

    4. Reya
      January 23, 2022 AT 4:20 pm

      5 stars
      I love this recipe, It is delicious and easy!

      1. Brittany Mullins
        January 24, 2022 AT 12:58 am

        So happy you enjoyed these muffins, Reya! Thanks for the review :).

    5. Marina
      September 26, 2021 AT 8:16 am

      5 stars
      Tehey are my so far favorite ones. Soooo good

      1. Brittany Mullins
        September 27, 2021 AT 10:52 am

        So glad you’re loving this recipe, Marina! Thanks so much for the review and star rating. I really appreciate it!

Parchment paper lined with protein balls.


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