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Gluten Free Lemon Poppy Seed Muffins

This one bowl, healthy and gluten free lemon poppy seed muffin recipe is made in just 35 minutes. These muffins are made with almond flour and tapioca flour and packed with lemon juice and zest, plus a dairy free lemon glaze on top. They are naturally sweetened with honey and maple sugar. And they’re the perfect little pick-me-up!

overhead image of muffins piled on a plate with glaze drizzled on top.

Disclaimer: We partnered with Bob’s Red Mill to bring you this post. We only work with companies and brands we truly believe in and use ourselves. Therefore, all opinions and recipes are entirely our own. Thank you for supporting The Real Simple Good Life and our partners.

What gluten free flour do you use to make these lemon poppy seed muffins?

For gluten free and Paleo friendly baking flours, we typically turn to Bob’s Red Mill and have for years. You’ll see us using their flours in lots of our recipes – from sweet like these healthy muffins to savory like our creamy Tuscan chicken! We love the quality of their products from mill to table and the fact that they’re a local Oregon company!

Straight on image of muffins piled on a plate with glaze drizzled on top.

For these healthy lemon poppy seed muffins, we used their Almond Flour and Tapioca Flour. Both flours are certified gluten free and non-gmo as well. The Almond Flour is made from whole, blanched almonds and this is important. You want blanched almond flour rather than almond meal for this recipe. Here’s why:

  • It’s finer and lighter and results in a fluffier texture.
  • It will give your muffins the yellow, lemony looking color. If you used almond meal the muffins would be more of a brown color.
Vertical image of three lemon poppy seed muffins stacked. Top muffin has a bite taken out of it.

Options for making these healthy lemon poppy seed muffins vegan friendly

These muffins can easily be make vegan friendly. Just note the color of the muffins will come out more brown than yellow. Here are some swaps you could make:

  • Eggs => use 3 flax eggs
  • Honey => use 1/3 cup maple syrup
  • Ghee => use 1/3 cup coconut oil
Vertical overhead image of lemon poppy seed muffins making an S shape on marble with extra glaze on the side.

Making the lemon glaze

You’ll want to note that we used traditional powdered cane sugar to make the lemon glaze white for these photos. If you want to stay refined sugar free, make sure to use powdered maple sugar instead. The glaze will turn out brown, but still tastes delicious! I think I actually prefer the flavor of the glaze with the maple sugar. To make it, you just pulse maple sugar in a high powered blender or food processor until powdery. You could also use coconut sugar – I can never seem to get it as fine as maple sugar though.

Vertical image of lemon poppy seed muffins piled on a plate with lemon glaze drizzled on top.

Other gluten free and healthy muffin recipes to try

Try these gluten free lemon poppy seed muffins

These healthy, gluten free lemon poppy seed muffins are great for meal prep to have on hand for snacks and treats. They are quick and easy to make, made in just 35 minutes and with one bowl for less cleanup, too! Leave a comment below to let us know how it goes. Also, take a pic to share on Instagram, and tag us @realsimplegood so we can check it out! Make sure to give us a follow if you don’t already – let’s stay connected!

Vertical image with text overlay at top. Lemon poppy seed muffins piled on a plate with lemon glaze drizzled on top.

Like this Recipe?


Vertical split image with text overlay in the middle. Top image is close up of one lemon poppy seed muffin with glaze drizzled on top. Bottom image is muffins piled on a plate with glazed drizzled on top.

Gluten Free Lemon Poppy Seed Muffins

4.67 from 18 votes
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 12 muffins
Author: Erica Winn
This one bowl, healthy and gluten free lemon poppy seed muffin recipe is made in just 35 minutes. Made with almond flour, tapioca flour and a lemon glaze!
Print Recipe Rate Recipe


Optional topping:

  • 1/2 cup powdered maple sugar (Pulse maple sugar in a high powered blender or food processor until powdery. Coconut sugar works or regular powdered sugar.)
  • 1 tbsp lemon juice (about 1/2 a lemon)


  • Preheat oven to 350° Fahrenheit and line a muffin pan with parchment liners.
  • In a large mixing bowl, whisk almond flour, tapioca flour, baking powder and sea salt. Make sure there are no clumps. Make a hole in the center of the flour mixture.
  • Add eggs, honey, lemon zest and juice, coconut oil and vanilla extract to the hole. Whisk and then combine the wet and dry ingredients until smooth, and fold in poppy seeds.
  • Scoop mixture into lined muffin tin, and transfer to oven. Bake for about 20 minutes, or until a toothpick comes out clean.
  • While the muffins cool, make optional topping if using. Whisk powdered maple sugar and lemon juice in a small bowl.
  • Once muffins have cooled, drizzle with topping and serve. Enjoy. Store in an airtight container on the counter or in the fridge to keep longer.
Tried this recipe?Take a picture and tag @realsimplegood so we can see it!

16 thoughts on “Gluten Free Lemon Poppy Seed Muffins

  • Wow! These are so delicious! I made them right after you posted, lol. Despite having a few setbacks (no baking powder, not enough almond flour, and not enough lemon juice) I made a couple of adjustments, and they still came out so dang good. I love the slight crust the tapioca gives the muffins, I like my baked goods a little crusty, and the tapioca flour achieves that for me. Four thumbs up! (Mine and hubbys)

    • Hooray! We are so happy to hear you both enjoyed these muffins!! We love the crisp, too! Thanks so much for jumping right on them and giving them a try! And thanks for coming back to share! 🙂

  • Just made these delicious babies and they are the best!!! I ran low on honey and added a little stevia. Thanks for creating amazing recipes!!

  • I made these without poppy seeds or icing and they were delicious! A huge hit with hubby and a great dessert treat 🙂 On the next batch I will add the icing.

  • These were really good! The lemon flavor really jumps out, which I love. I skipped the glaze because I didn’t have maple sugar, but just did a tiny drizzle of honey instead. These muffins are a fun little treat for the morning.

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