Gluten Free Lemon Poppy Seed Muffins
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Last updated on Feb 26, 2025
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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.
If you’re as lemon-obsessed as I am, you’ll also want to try my healthy lemon loaf, lemon almond flour cookies, and healthy lemon bars. Each of these recipes brings a unique twist to classic lemon desserts, and I can’t wait for you to try them!
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 healthy lemon poppy seed 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
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 – helps 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.
Substitutions
- Vegan muffins: If you need an egg-free option, try flax eggs (1 Tablespoon ground flax + 2.5 Tablespoons water per egg). The texture will be slightly different, but it should still work.
- Sugar swap: You could use maple sugar, date sugar, or regular cane sugar if needed. Each will bring a slightly different flavor, but all will keep the muffins sweet and delicious.
- Use a different oil: Melted butter, ghee, avocado oil, or even applesauce can be used in place of coconut oil. If using butter or ghee, expect a richer, more classic muffin flavor.
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!
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.
Frequently Asked Questions
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.
If your muffins came out too dense, it could be due to overmixing the batter or using too much coconut flour, which absorbs a lot of liquid. Make sure to measure the flours correctly and mix just until combined for the best texture.
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!
These muffins were specifically developed to be gluten-free, but if you want to experiment, you could try using all-purpose flour in place of both almond and coconut flour. You may need to adjust the liquid, as coconut flour is much more absorbent.
More Spring Recipes to Try
- Healthy Lemon Bars
- Blueberry Yogurt Muffins
- Lemon Almond Flour Cookies
- Oatmeal Carrot Cake
- Healthy Carrot Raisin Muffins
Be sure to check out all of my muffin recipes on EBF!
If you enjoyed this recipe, please consider leaving a ⭐ star rating and let me know how it went in the 📝 comments below.
Lemon Poppyseed Muffins
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
- ½ cup powdered sugar
- 1 Tablespoon lemon juice
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
- Recipe inspired and adapted from this Keto Lemon Cake.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
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?!?
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.
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 😉
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!
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..
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!
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.
I know that problem often, Holly 🙂 So glad you’re enjoying these muffins, thanks for making them and leaving a review!
Very tasty! Almost too much poppy seeds…. But still very good!
Glad you liked these muffins, Trova! I appreciate your review 🙂