Coconut Flour Lemon Poppy Seed Muffins with Creamy Lemon Icing

These Coconut Flour Lemon Poppy Seed Muffins have the perfect balance of sweet and tart flavors, and are naturally gluten-free with plenty of protein to leave you feeling satisfied.

coconut flour lemon poppyseed muffins with lemon icing drizzled on top

I love adding freshly squeezed lemon juice to baked goods, as it’s refreshing and loaded with vitamin C and potassium, along with other nutrients like iron and magnesium. Poppy seeds add a mild crunch in this recipe, and also contribute a small dose of calcium, iron, and zinc in each bite. Even my toddler son, who typically doesn’t care for add-ins in his muffins and cookies, loves to bite into these light and fluffy lemon poppy seed muffins!

coconut flour lemon poppyseed muffin with lemon icing broken in half

These Coconut Flour Lemon Poppy Seed Muffins are:

  • gluten-free and grain-free
  • dairy-free
  • nut-free (if you omit the icing)
  • naturally sweetened
  • light and fluffy
  • higher in protein and lower in sugar than a traditional muffin
  • take only 15 minutes to prepare before baking

You can serve these fluffy muffins as is, or you can top them with the Creamy Lemon Icing recipe I’ve included for a slightly sweeter and fancier presentation. The icing is not nut-free, so keep that in mind if any of your friends or family members have allergies, but it’s quick to prepare and makes these muffins feel more like a cupcake to serve at a special occasion! This is not the type of icing that will harden, since it doesn’t contain refined powdered sugar, so be sure to add the topping right before serving for best results.

lemon icing being drizzled over coconut flour lemon poppyseed muffins

4.73 from 11 votes
Coconut Flour Lemon Poppy Seed Muffins with Creamy Lemon Icing
Prep Time
10 mins
Cook Time
25 mins
Total Time
35 mins

The best Coconut Flour Lemon Poppy Seed Muffins I've ever tasted! They're gluten-free, dairy-free, and Paleo, with a creamy vegan icing.

Course: Dessert
Servings: 12
Calories: 135 kcal
Lemon Poppy Seed Muffins:
  • 3/4 cup coconut flour (level measurement, not heaping)
  • 3/4 cup maple syrup , at room temperature
  • 1/4 cup melted coconut oil
  • 6 tablespoons freshly squeezed lemon juice
  • Zest of a whole lemon (about a teaspoon)
  • 1/4 teaspoon salt
  • 1 teaspoon baking soda
  • 6 eggs , at room temperature
  • 1 teaspoon vanilla extract
  • 2 tablespoons poppy seeds
Creamy Lemon Glaze:
  • 1/4 cup raw cashew butter
  • 2 tablespoons pure maple syrup
  • 2 teaspoons fresh lemon juice
  • 1 to 3 teaspoons water , as needed to thin
  1. Preheat the oven to 350ºF and line a standard muffin tin with 12 baking cups. (I use these silicone liners for best stick prevention.)
  2. Make sure your maple syrup and eggs are at room temperature. You can place the eggs in a bowl of warm tap water for a few minutes to help warm them up quickly. This will ensure that your muffin batter will be runny, like traditional muffin batter, and will easily mix and pour into the muffin cups. (Otherwise the coconut oil may harden and won't mix evenly into the batter.) In a large bowl, combine the coconut flour, maple syrup, coconut oil, lemon juice and zest, salt, baking soda, eggs, and vanilla, and use a whisk to stir the batter until smooth. The whisk should help break up any clumps, making the batter very smooth. Stir in the poppy seeds, then divide the batter evenly among the 12 baking cups.
  3. Bake at 350ºF until the centers are firm to the touch and the edges are lightly golden, about 22 to 25 minutes. Cool completely before topping with the icing below.
  4. To prepare the Creamy Lemon Icing, stir together the cashew butter, maple syrup, and lemon juice in a small bowl until smooth. Add water 1 teaspoon at a time, as needed to thin the icing to your liking. Drizzle it over the top of each muffin just before serving.
  5. Leftover muffins can be stored in an airtight container in the fridge for up to a week.

poppy seeds mixed into lemon muffin batter and coconut flour lemon poppyseed muffins in muffin tin

Substitution notes: 

  • Flour: Since the muffins are made with coconut flour, I don’t recommend making many modifications to this recipe– coconut flour is SO tricky to work with and cannot be substituted for all-purpose flour, almond flour, or any other flour that I know of. If you’re put-off by the amount of eggs this recipe calls for, you could try substituting a 1/4 cup of applesauce or a flax or chia egg for 1 of the eggs in this recipe, but I wouldn’t stray too far from the number of eggs called for, as they provide the structure of this recipe. Flax and chia eggs rarely work in coconut flour recipes because they don’t rise and firm up in the same manner that chicken eggs do. If you do decide to try working with a vegan egg, make sure you’re prepared for a different results– the centers of the muffins might remain gooey inside.
  • Sweetener: I did try making this recipe with coconut sugar instead of maple syrup, and the results are much darker in color, less sweet, and overall not as pretty.  The maple syrup provided a muffin that looks more traditional, as you see pictured in this post. 
  • Nut-Free: If you’d like to try a nut-free option for the Creamy Lemon Icing, I’d try using coconut butter instead of the raw cashew butter. Just taste as you go and adjust the flavor and texture as needed. 

Reader Feedback: Do you have a favorite baked good for Spring? Let me know if you have any healthy makeover requests!





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There were fabulous. Moist. Not dense like some gluten free are. I made mini muffins which are the perfect snack size. Follow recipe exactly as is except I substituted hiney for maple syrup. Same amount. Tasted fine and so moist.


I made these today and they were a HIT with my husband and two kids. I was afraid they might be to “eggy” for their taste, but none of them noticed at all, and all of them came back begging for another one. I actually don’t have a zester, so I tried to scrape as much zest as I could with a cheese grater, but it was barely an eighth of a teaspoon. I also ran out of maple syrup (was about 1/8 cup short), but added some honey into it to make up for the difference, and even with these unintended modifications, the muffins were excellent!


I am dieting because of some health issues.
I was craving for some healthy dessert so I made these yesterday, and I love it.
I just replaced the poppy seed to chia seeds (since I had them at home) and it was perfect.
Thanks so much for your recipe.


Would a ‘flax-egg’ work in this recipe? Thanks

    Megan Gilmore

    My guess is no. Usually flax eggs work best in recipes that call for grain-based flours and only call for 1-2 eggs. When you use them with coconut flour, the result is usually very gooey and under-baked in texture.


Hi. Would it make a difference if u would replace the eggs with flax or chia n also use xanthum gum n maybe baking powder? Would this combo work ?


Omg just made these and eating one now as im typing. Sooooooo gooood

JoAnn Billitti

Have you tried these in a loaf pan; if so, how long to bake? I like that better than muffins as it’s easier to slice and toast.
really enjoy your recipes



    Megan Gilmore

    Grain-free muffins will often lose their initial dome-shaped tops when they cool, turning into more of a flat muffin top. I think that’s just the nature of not baking with wheat flour. As long as the centers are baked through, they should be good!

      Bridget Chase

      they didn’t just level off, they were concave, so I’m not sure what happened. They were still delicious so I will give it another attempt.


These are so good! Even the kids and hubby love them! I didnt have poppyseeds so i used chia. I also used honey in place of mapLe syrup. Ill deinitely be making these agAin!

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