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.

If you make these lemon poppyseed muffins, be sure to leave a comment and star rating letting me know how they turned out! Your feedback is so helpful for the EBF team and other EBF readers.

Print

Lemon Poppyseed Muffins


  • Author: Brittany Mullins
  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Total Time: 40 minutes
  • Yield: 12
  • Diet: Gluten Free

Description

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.


Ingredients

  • 5 eggs (at room temp)
  • 3/4 cup coconut sugar
  • 1/2 cup coconut oil (liquid state/melted)
  • 1/4 cup lemon juice (at room temp)
  • 1/2 Tablespoon lemon zest
  • 2 cups almond flour 
  • 1/4 cup coconut flour 
  • 1 Tablespoon baking powder
  • 2 Tablespoons poppy seeds 
  • lemon glaze (optional)

Lemon Glaze 

  • 1/2 cup powdered sugar
  • 1 Tablespoon lemon juice

Instructions

  1. Preheat oven to 350°F. Place 12 paper or silicone liners in your muffin tin. 
  2. 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. 
  3. 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. 
  4. 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.
  5. Let muffins cool in the tin for about 10 minutes or so, then remove and let cool completely on a wire rack. 
  6. 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.
  7. Drizzle glaze over each muffin just before serving. 
  8. Store muffins and glaze in separate storage containers in the fridge for up to 5 days. 

Notes

  • 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.
  • Category: Breakfast
  • Method: Bake
  • Cuisine: American

Nutrition

  • Serving Size: 1 muffin (without glaze)
  • Calories: 291
  • Sugar: 16g
  • Sodium: 163mg
  • Fat: 21g
  • Saturated Fat: 9g
  • Unsaturated Fat: 2g
  • Trans Fat: 0g
  • Carbohydrates: 28g
  • Fiber: 3g
  • Protein: 7g
  • Cholesterol: 77mg

Keywords: lemon poppyseed muffins

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    37 comments
  1. These muffins are SO good! I made them for my mom’s birthday since she loves lemon poppyseed, and they turned out perfectly. 🙂 The taste is very well balanced and the muffins are nice and moist!

    • Woo-hoo!! So glad these muffins were a hit, Danielle. I appreciate you making them and taking the time to leave a comment + star rating. The reviews are super helpful to other readers, so I appreciate it. 🙂

  2. Can the coconut and almond flour be substituted for just regular white flour? Do you need to use coconut oil, or can that also be substituted with something else?

    • Hey Celine – Some people have subbed the coconut flour for AP flour, but I’m not sure how it’d turn out subbing all the flour for regular flour. I’m sure it’d work just fine, but I haven’t tried it so I’m not 100% sure. Someone subbed the coconut oil for applesauce and said it worked perfectly!

    • Ahh yay!! So glad these muffins turned out for you, Toni. And good to know they worked with 2 flax eggs instead of regular eggs. 🙂 Thanks for taking the time to leave a comment + star rating. I so appreciate it!

  3. Made the lemon poppy seed muffins (well I made them into donuts and mini muffins for my little one.) Hands down amazing! Texture was so on point. Flavor out of this world! Super easy recipe to follow. Will be making again. Ty!!

    • Ahh yay, that makes me so happy to hear, Melanie!! I love that you turned these into donuts and mini muffins. 🙂 Thanks for trying my recipe and for coming back to leave a comment + star rating. It means the world to me!

  4. The best muffins I have had in a long time! I highly recommend making these and I will 100% be making them again. Thanks!

    • Ahh that makes me so happy to hear, Sophia!! I’m so glad you enjoyed these muffins. Thanks for trying my recipe and for coming back to leave a comment + star rating. I so appreciate it!

  5. Love these! I modified a few things but they still turned out great. Here’s what I modified (because I find comments from others super helpful!)
    — 1/2 cup unsweetened applesauce instead of coconut oil
    — 3 whole eggs and 6 tbsp of liquid egg whites (3tbsp for each whole egg I omitted)
    — 1/4 cup arrowroot powder/flour instead of coconut flour (because I didn’t have any. Arrowroot is still gluten free!)
    — chia seeds in place of poppy seeds as others have mentioned
    Yum!! Thanks for the recipe!

    • Ahh yay!! I’m so glad you enjoyed this recipe, Kimberly. Thanks for coming back to leave a comment and star rating and thanks for sharing the substitutions you made. They are super helpful for other readers!!

    • Ahh that makes me so happy to hear, Nicole!! I’m so glad you guys enjoyed these muffins. Thanks for trying my recipe and for coming back to leave a comment + star rating. I really appreciate it!

  6. These muffins blew us away. Gorgeous, delicious, healthy, & GF? Yes! The catch is that the glaze is just too amazing & these are SO delicious we can’t stop eating them! Thank you so much for another winner!!!

    • Ahh this makes me so happy to read, Jennifer!! I’m so glad these muffins were a hit. Thanks for trying them and for coming back to leave a comment + star rating. It means the world to me. <3

  7. These were AMAZING! I accidentally ate 2 in 5 minutes:)

    So fluffy and great with or without the lemon glaze! Definitely one of my favorites!!

  8. I used 5 tablespoons of ground up chia ‘chia egg’ to make it vegan and it was so good! Probably not as fluffy but still excellent. Thank you!

    • Oh yay!! I’m so happy to hear that the muffins still worked with flax eggs. Thanks for letting me know. 🙂 And thanks for coming back to leave a comment + star rating. I really appreciate it!

  9. The flavor on these is delicious, perfect for spring! They have a nice cake-y texture and I like that a hint of coconut comes through. I added 1/4 tsp each of almond and vanilla extract and used chia seeds instead of poppy. I also replaced half the oil with applesauce.

    As warned, my eggs and applesauce were too cold so the coconut oil hardened up…but I just kept mixing and they still turned out really well. Thank you!

  10. If I cut the sugar down will it make a big difference in taste? I would like my kids to be able to eat these but less sugar.

  11. Oh. My. Gosh. These were ridiculously delicious! Thank you SO much for all your recipes. I didn’t have poppyseeds or coconut flour (so I just used white flour to replace the coconut), and I added way more lemon juice and coconut flakes on the top :p. But guys. Brittany never disappoints 😍

    • Ahh yay!! I’m so glad you enjoyed these muffins!! 🙂 Good to know that they worked when you subbed white flour for the coconut flour. Did you just use the same amount of white flour as what’s called for in the recipe for the coconut flour?

  12. I made this last night and it was so delicious, my boyfriend ate 60% of it in one sitting. Because it’s not an easy time to run to the market for an ingredient, I subbed the 1/4 cup coconut flour with an all purpose 1 for 1 gluten free flour that is mostly rice and tapioca based and it worked fine! I didn’t change any other ingredients but I made this in a pyrex loaf pan so I lowered the temp in the oven to 330 and baked for 55 min. Perfect!

    • Ohh yay, I’m so glad these muffins were a hit!! Good to know that they worked with the AP GF flour instead of the coconut flour. Thanks for letting me know and for coming back to leave a comment and star rating, Erin. The reviews are super helpful to other readers, so I really appreciate it. <3

  13. The recipe looks great. However, if you cannot use almond flour due to nut allergies what flour would you recommend as a substitute? Please let me knw.o Thank you.

    • Hey Sharon! I haven’t tried using another type of flour for these muffins, so I’m not sure. You could test out all-purpose flour or GF AP flour to see how they turn out, but again I haven’t tried it so I’m not sure if they’ll turn out the same. Let me know if you end up trying it and how they turn out!

  14. Can you substitute all purpose gluten free flour plus regular vegetable oil for coconut oil? I have several family members allergic to coconut

    • Hey Tammy – It should be fine to swap out the coconut oil with vegetable oil. As far as the flour goes, I haven’t tried using AP GF flour so I’m not sure how the muffins will turn out. Feel free to experiment though and definitely report back if you end up trying them!

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