Gluten-Free Lemon Poppyseed Muffins



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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.

More Lemon-Based Baked Goods

Try These Muffin Recipes

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

4.59 from 39 votes

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.
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

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakfast
Cuisine: American
Keyword: lemon poppyseed muffins
Did you make this recipe?Mention @eatingbirdfood and tag #eatingbirdfood!

About Brittany

Hey there, I’m Brittany, the creator of Eating Bird Food, cookbook author, health coach and mama of two littles. Here you’ll find quick and easy recipes that make healthy fun and enjoyable for you and your family!

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Recipe Rating


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

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