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Home » Grain Free Recipes

Grain Free Lemon Poppy Seed Muffins Made with Almond Flour

Nov 17, 2025 by Thriving Gluten Free · This post may contain affiliate links · 10 Comments

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These Almond Flour Lemon Poppy Seed Muffins will brighten up anyone's day! They're packed with protein, loaded with fresh lemon flavor, crunchy poppy seeds, then topped with a sweet and tangy homemade lemon glaze. Perfect for a dessert, snack or lunch box treat!

grain fee lemon poppy seed muffins recipe made with almond flour

Grain Free Lemon Poppy Seed Muffins

Lemon Poppy Seed is a classic, and it's one of my all time favorite flavors! This grain-free version is made with "better for you" ingredients, but still tastes incredible. They're light and fluffy, packed with protein and lots of sunshiny lemon flavor!

What ingredients do I need to make this Almond Flour Lemon Poppy Seed Muffins Recipe?

Here's what you'll need:

  • Almond Flour. Be sure to use a superfine almond flour.
  • Eggs. You'll need 3 eggs. It may seem like a lot, but you need them to help with binding and I promise the muffins don't taste eggy at all.
  • Coconut Sugar. Regular granulated sugar works fine too.
  • Salt
  • Baking Powder
  • Pure Vanilla Extract
  • Fresh Lemons. You'll need a couple of these!
  • Poppy Seeds. You can also sub chia seeds!

For the lemon glaze recipe, all you'll need is confectioners sugar and some more fresh squeezed lemon juice.

Looking for more ways to use almond flour? I think you'll love these delicious recipes, too!

  • Almond Flour Banana Muffins
  • Easy Almond Flour Crepes
  • Almond Flour Waffles

How to Make These Gluten-Free Lemon Poppy Seed Muffins

Preheat the oven and prep your muffin pan by greasing.

Start by adding the wet ingredients to a mixing bowl and blend them together.

Combine the dry ingredients in a separate small bowl, then slowly add them to the wet ingredients until well combined.

Finally stir in the poppy seeds then fill the muffin cups about two-thirds full with batter. Bake until golden brown about 20-25 minutes.

Homemade Lemon Glaze Recipe

Making the lemon glaze for these muffins is completely optional. They're bursting with flavor on their own, but I would highly recommend you go all out and add the glaze, especially if serving them for dessert. It takes 2 minutes to combine the confectioners sugar and lemon juice, and it really takes these muffins to the next level!

Have you tried this recipe? Be sure to leave a comment below and tag me on Instagram @thrivingglutenfree so I can see how it turned out!

Get your muffin pan ready and let's bake!

gluten free grain free lemon poppy seed muffins recipe made with almond flour
4.50 from 2 votes
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Grain Free Lemon Poppy Seed Muffins Made with Almond Flour

These simple and delicious Almond Flour Lemon Poppy Seed Muffins will brighten up anyone's day! They're packed with protein, loaded with fresh lemon flavor, crunchy poppy seeds, then topped with a sweet and tangy homemade lemon glaze. Perfect for a dessert, snack or lunch box treat!
Prep Time10 minutes mins
Cook Time20 minutes mins
Total Time30 minutes mins
Course: Dessert
Cuisine: American, gluten-free
Keyword: Almond Flour, lemon, poppyseed
Servings: 12 regular size or 24 mini muffins

Equipment

  • 1 Muffin Pan

Ingredients

  • 2 cups Almond Flour
  • 2 teaspoon Baking Powder
  • 3 Eggs
  • ½ cup Coconut Sugar or sweetener of choice
  • 1 teaspoon Pure Vanilla Extract
  • 3 tablespoon Fresh Lemon Juice about 1 lemon
  • 2 teaspoon Lemon Zest
  • ¼ cup Coconut Oil melted
  • ¼ teaspoon Salt
  • 1 tablespoon Poppy Seeds can sub chia seeds!

Lemon Glaze- Optional, but I think it's necessary 😉

  • 1 cup Confectioner's Sugar
  • 2-3 tablespoon Fresh Lemon Juice

Instructions

  • Preheat oven to 350°
  • Add the wet ingredients to a mixing bowl and blend well.
  • Combine the dry ingredients in a medium bowl.
  • Slowly mix the dry ingredients into the wet. Mix until well combined, but do not over mix.
  • Stir in the poppyseeds
  • Grease muffin tin and fill two-thirds with batter.
  • Bake 20-25 minutes or until golden brown. If making mini muffins, shorten the cooking time to about 12-14 minutes.
  • Let cool, then drizzle with lemon glaze.

Lemon Glaze

  • In a small bowl combine sugar and lemon juice. Stir until smooth.
  • To thin the glaze, add more lemon juice until desired consistency is reached. To thicken, add more sugar.
Tried this recipe?Mention @thrivingglutenfree or #thrivingglutenfree!

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    The Best Loaded Baked Potato Casserole with Bacon and Cheddar
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    Fudgy Almond Flour Brownies
  • gluten free coconut macaroons recipe
    Gluten Free Flourless Coconut Macaroons
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    Bacon Wrapped Jalapeño Poppers (Easy Appetizer!)

Comments

  1. Bell says

    November 17, 2025 at 7:12 pm

    5 stars
    These grain-free lemon poppy seed muffins turned out so moist and delicious! The almond flour gives them the perfect texture, and the lemon flavor is bright and refreshing. Definitely a new favorite! My son usually doesn’t like poppy seeds, but he loved these muffins. I didn’t add the glaze because I didn’t want them any sweeter the muffins have a perfect balance just as they are.

    Reply
    • Thriving Gluten Free says

      November 24, 2025 at 6:37 am

      So happy you loved the recipe! Always a win when the kiddos love something, too 🙂 Thank you so much for sharing!

      Reply
  2. Donna says

    April 10, 2025 at 6:21 pm

    These are amazing🍋 thanks

    Reply
    • Thriving Gluten Free says

      April 11, 2025 at 11:47 am

      So happy to hear that you enjoyed the recipe!!

      Reply
  3. Jane says

    March 01, 2023 at 3:29 pm

    4 stars
    Easy to make; came out perfect—not too sweet; the glaze adds some sweetness
    which is nice. Watch to make sure they don’t over bake as almond flour browns quick.
    Mine were done at 18 min.

    Reply
    • ThrivingGlutenFree says

      March 19, 2023 at 8:32 am

      So happy you enjoyed the recipe! Thanks for sharing!

      Reply
  4. Sandy says

    January 14, 2023 at 12:22 pm

    In your dialogue about making the muffins you state “ you will need 4 eggs” but then in the actual recipe it lists only 3 eggs.

    Reply
    • ThrivingGlutenFree says

      April 24, 2023 at 9:17 pm

      Thanks for catching that! You only need 3 eggs 🙂

      Reply
  5. Cheryl Greninger says

    May 25, 2022 at 12:30 am

    My problem is that, when I melt the coconut oil, then add in other wet ingredients, the coconut oil solidifies. So, I have big lumps of coconut oil. How do you prevent that from happening?

    Reply
    • Thriving Gluten Free says

      June 07, 2023 at 11:34 pm

      The best way to prevent this from happening is to bring other ingredients to room temperature before mixing in the coconut oil. Feel free to use another oil instead like avocado oil if you prefer not to use coconut oil.

      Reply
4.50 from 2 votes

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thriving gluten free recipes for those with celiac disease and gluten intolerance

Hi, I'm Debby! The recipe creator, mom and blogger behind Thriving Gluten Free. Our oldest daughter was diagnosed with Celiac Disease in 2011, so we've been navigating gluten-free living ever since. I love to share our favorite recipes, products and tips to help make your gluten-free life easy, healthy and delicious!

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