Gluten Free Lemon Poppy Seed Muffins

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These gluten free lemon poppy seed muffins are made with almond and coconut flour and have a bright, lemony flavor. They’re delicious as is or topped with a lemon glaze!

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 gluten free lemon poppy seed 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.

Why I Love These Muffins

  • Gluten-Free – Made with almond and coconut flours, these muffins are a safe and delicious option for those avoiding gluten.
  • Easy – They’re easy to make with only 9 simple ingredients!
  • Versatile – These muffins are a great snack or breakfast option to meal prep for the week, but they also make for a great addition to Easter or Mother’s Day brunch.

// ★★★★★ Review //

“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!!”Erin

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

Ingredients Needed

  • eggs – you’ll want your eggs to be at room temperature, otherwise if they’re too cold they could cause the coconut oil to harden up.
  • coconut sugar – instead of granulated sugar or brown sugar we’re using coconut sugar, which offers a natural sweetness with a hint of caramel-like flavor.
  • coconut oil – in its liquid state to blend easily into the mix, adding moisture and a slight coconut aroma.
  • lemon juice and zest – for that vibrant, citrusy tang that defines the muffins.
  • almond flour – provides a gluten-free base, adding a nutty flavor and tender crumb.
  • coconut flour – absorbs moisture, helping to achieve the perfect texture while keeping it gluten-free.
  • baking powder – ensures the muffins rise beautifully as they bake.
  • poppy seeds – add a light crunch and visual appeal to every bite. While these muffins are called poppy seed muffins, if you don’t have any poppy seeds on hand others have used chia seeds and said they work well.
  • lemon glaze – an optional, but highly recommended topping! The glaze takes these muffins to the next level.
Mixing bowl with lemon poppyseed muffin batter.

How to Make Gluten Free Lemon Poppy Seed Muffins

Step 1: In a medium mixing bowl whisk the eggs, coconut sugar, melted coconut oil, lemon juice and zest in a bowl.

Step 2: In a separate large mixing bowl, mix almond flour, coconut flour, baking powder and poppy seeds. Add the wet ingredients to the dry ingredients and mix until smooth.

Step 3: Fill prepared muffin cups ⅔ full and bake for 23-25 minutes. Let the muffins cool in the tin for 10 minutes, then move to a wire rack.

Step 4: If making the glaze, whisk the powdered sugar and lemon juice together until smooth. Drizzle glaze over cooled muffins and enjoy!

Brittany’s Recipe Tips

  • Sift the flours: Coconut and almond flours tend to clump. Sifting them before adding to the mix can help achieve a smoother batter and more uniform muffins.
  • Use room temperature ingredients: 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. Ah baking… a balancing act!
  • Use muffin liners: If using muffin liners I highly recommend using silicone muffin liners or parchment baking cups for the best results and to prevent the muffins from sticking. If using paper ones, you might want to spray them with non-stick spray otherwise the muffins could stick.
  • Let cool completely: I can’t stress this enough. Let your muffins 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!
Lemon poppyseed muffins on a plate. One has a bite taken out of it.

How to Store Lemon Poppy Seed Muffins

  • At room temperature: Store in an airtight container on the counter for 1-2 days.
  • In the fridge: These muffins will stay fresh for up to 5 days when refrigerated in an airtight container.
  • In the freezer: Let the muffins cool completely, then transfer them to a freezer-safe container and store for up to 3 months. If storing in the freezer I recommend storing without the glaze. When ready to enjoy, let them thaw in the fridge overnight and add the glaze if desired.
Plate with lemon poppyseed muffins topped with lemon zest and a glaze.

Frequently Asked Questions

Can I make these muffins egg-free or vegan?

I haven’t tried it, but other readers have used flax eggs and said the muffins turned out great! To do this, substitute each egg with a flax egg (1 tablespoon ground flaxseed mixed with 3 tablespoons of water, let sit for 15 minutes). Keep in mind the texture may vary slightly.

Is there a substitute for coconut sugar?

Absolutely. You can use an equal amount of raw sugar, or for a sugar-free version, use a granulated sweetener like erythritol or a liquid stevia to taste.

Can I use another type of oil instead of coconut oil?

Yes, melted unsalted butter (if not dairy-free) or another neutral oil like avocado oil can be used in place of coconut oil. Others have also used applesauce as a substitute for the oil and said it worked well.

Can these muffins be made into a loaf instead?

Yes, you can bake this batter in a loaf pan. Adjust the baking time to about 45-55 minutes, or until a toothpick comes out clean from the center. You can also try making my lemon loaf instead!

More Spring Recipes to Try

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

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4.60 from 40 votes

Lemon Poppyseed Muffins

These gluten free lemon poppy seed muffins are made with almond and coconut flour and have a bright, lemony flavor. They're delicious as is or topped with a lemon glaze!
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes
Servings: 12

Ingredients  

  • 5 eggs, at room temperature
  • ¾ cup coconut sugar
  • ½ cup melted coconut oil
  • ¼ cup lemon juice, at room temperature
  • 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 

Instructions 

  • 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. 

Video

Notes

Nutrition

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: gluten free lemon poppy seed 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




69 Comments

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

    1. 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!

  2. 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.

    1. 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!

  3. 5 stars
    These were really great! I had fun making and even more fun eating them. Wonderful recipe!

    1. Ahh yay!! I’m so glad you enjoyed this recipe, Albertina. Thanks for trying it and for coming back to leave a comment and star rating. I really appreciate it. <3

  4. 5 stars
    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!

    1. 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

  5. 5 stars
    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 😍

    1. 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?

  6. 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.

    1. Hey Mel – I think that’d be fine to cut the sugar down! Let me know how they turn out for you if you end up making these.

  7. 5 stars
    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!

    1. So glad these muffins turned out for you, Sophie!! Thanks for trying them and for coming back to leave a comment and star rating. I really appreciate it!!

  8. 5 stars
    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!

    1. 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. 5 stars
    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!!

    1. Haha you’re not alone, Erin. 🙂 I’m so glad you enjoyed these muffins!! Thanks for trying my recipe and for coming back to leave a comment and star rating. I really appreciate it.

  10. 5 stars
    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!!!

    1. 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

    1. 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!

  11. 5 stars
    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!

    1. 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!!

  12. 5 stars
    The best muffins I have had in a long time! I highly recommend making these and I will 100% be making them again. Thanks!

    1. 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!

  13. 5 stars
    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!!

    1. 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!

    1. 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!

  14. 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?

    1. 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!

  15. 5 stars
    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!

    1. 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. 🙂

    1. Hi Sarah! You could certainly try that, but I haven’t tested it so I don’t know how they would turn out. Let me know if you experiment.

  16. 5 stars
    I made these today. Substituted brown sugar for coconut sugar. They came out deliciously light and beautiful.

    1. Woo! So glad this recipe was a hit! Thanks for making them and for coming back to leave a review. I so appreciate it, Michaela!

  17. 5 stars
    Recipe for gluten free poppyseed lemon cupcakes/ muffins turned out really well. My three year old and I made them together. I had my reservations as I have not had lot of experience baking with these gluten free ingredients before. Well I am so impressed with how good these are! Will be making these again for sure. thank you

    1. So glad these turned out for you, Erin! Thanks for making them and for the review. I so appreciate it!

  18. I just made these and turned out great! I swapped coconut sugar to brown sugar replacement (Swerve) and they’re so delicious & fluffy.

    1. So glad these muffins turned out for you, Veronica!! Thanks for making them and for the review. I so appreciate it.

  19. 5 stars
    I have made SEVERAL of your muffin recipes (muffins = my toddlers life). She LOVED them. I used the swerve confectioners sugar to make the icing. It was hard to get the right consistency without the lemon juice over powering and making it too tart. The muffins were absolutely delicious. Will be making again for Mother’s Day.

    1. So glad these muffins were a hit!! Thanks so much for making my recipe and for coming back to leave a review. I so appreciate it!

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

    1. 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.

  20. 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!

  21. Hi Mrs. Brittany, what do you think I could replace the coconut sugar and egg? Do you think Bob’s Red Mill egg replacer or flaxmeal be good? ( for it ) Thanks..

    1. Hi Claire – 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. Let me know how they turn out for you!

  22. Hi😁 What would the measurements be if I were to use regular/white flour & olive oil in place of coconut oil ?
    I ask because I’m not on a glutton free diet & im not familiar with baking with coconut oil.
    Just curious, as I love lemon-poppyseed muffins 😉

    1. Hi Monica. I don’t recommend subbing the flour in this recipe, but you can use melted unsalted butter (if not dairy-free) or another neutral oil like avocado oil can be used in place of coconut oil. Hope you enjoy these muffins!

  23. So I was truly excited to see upon opening that this recipe was supposedly GF AND V, being that I’m allergic to both. Well when jumping to the recipe and seeing that the first ingredient listed is 5 EGGS, I’m a little perplexed and greatly disappointed or at least trying to figure out when eggs became vegetarian or vegan?!?

    1. Hi Jennifer. This recipe is GF and vegetarian but it isn’t vegan. Vegetarians will typically eat egg products unless they have chosen not to eat animal products. Hope that helps answer your questions.