Coconut Flour Lemon Poppy Seed Muffins with Creamy Lemon Icing

It’s starting to feel like Spring around here, so these Coconut Flour Lemon Poppy Seed Muffins seem like a delicious way to celebrate. They’ve got the perfect balance of sweet and tart flavors, and are naturally gluten-free with plenty of protein to leave you feeling satisfied.

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!

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.

4.67 from 3 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.

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!




Meet Megan Gilmore

Hi, I’m Megan. A former fast food junkie turned certified nutritionist consultant, trying to make healthy living as easy as possible. I believe in eating delicious whole foods on a regular basis to help naturally support the body’s detox organs— no juice fasting required. (Unless you want to!) If you make one of my healthy recipes, tag @detoxinista on Instagram or Facebook so I can see!

17 thoughts on “Coconut Flour Lemon Poppy Seed Muffins with Creamy Lemon Icing

  1. Laura ~ Raise Your Garden

    I love how you managed to make these higher in protein and lower in sugar. White sugar is the enemy these days, but I don’t want to deprive myself entirely either. Was just reading that in just a few years 1/3 of Americans will be clinically diabetic (not to mention obese). I ate zero white sugar and flour for months so I’d pass my 1 hour glucose test. Fascinating that most woman fail that now. Makes you wonder what changed over the years?

  2. Anna

    Looks yummy! I see you don’t reccommend straying from the recipe as coconut flour is tempermental 😉 as a general question do you ever use a date/water paste instead of maple syrup as a fruit sweetener? Trying to avoid all sugars for a bit, except fruit sugars.
    Thank you :)! Love and appreciate your recipes online and in your cookbooks!!

  3. Caitie

    These look awesome! I’ve been loving your recipes for years 🙂 I saw you mentioned that you tried with coconut sugar and it wasn’t quite the same, but I was wondering if you have any recommendations for making it sugar-free? Maybe stevia or monkfruit? I have chronic candida issues so I try to keep things sugar-free when I can. Thanks!! <3

  4. Kathryn

    These look wonderful!! Like Rachel, I’d like to make them egg-free, and am wondering if flax eggs would work, but I’m not sure if I can get away with replacing 6 eggs with flax eggs!

  5. Susan

    These are the best paleo muffins I’ve ever had! I normally don’t love the flavor of coconut flour and eggy muffins, but the lemon in these is what stands out. As the batter is very thin, I ended up blending everything together, except the poppyseeds, in my Vitamix, and just stirred the poppyseeds in afterward – no need to warm the eggs or melt the oil.

    Thanks for such an easy and delicious recipe – it’s a keeper!

  6. Jill

    I actually love the high number of eggs to get more protein for my toddler who is very picky. Thank you, i look forward to trying this recipe! (I was thinking of using chia seeds as i don’t have poppy seeds on hand…)

  7. Karen

    Megan, this recipe looks delicious! I own both of your cookbooks and have enjoyed making many of your online recipes as well. Have you tried making this recipe in a cake? If so, how long would you bake it for and what pan size would you use?

    1. Megan Gilmore Post author

      I haven’t tried it as a cake yet, but I would guess it would fill a standard 9-inch round cake pan. Maybe around 30 minutes for baking? Just check the center for firmness to make sure it’s cooked through– you should be able to smell the cake very fragrantly in your home as it starts to approach done-ness, so that’s usually when I know to start checking on it. 😉

  8. Anne

    Perfect timing! I need to use up my poppyseeds before I move and this recipe is way healthier than the other one I have. I’ll make these next week!

  9. Gulajawa

    Hi Megan,

    enjoys reading your recipes and I’ve tried to bake it. Basically we like lemon so it was really delicious and I love the smell of lemon in the cake, … thumbs up for your recipe ^ _ ^

  10. Molly

    I made them in a silicone muffin tray greased with coconut oil. The bottoms stuck a bit, but they were overall delicious. I loved them. My partner said ‘they remind him of the ones they set out at conferences, but don’t leave you feeling like you ate a brick’.

  11. Jessica

    Hi Megan!
    I tried making these tonight and the egg separated a bit from the rest of the mixture when I baked them. They still taste great but at the bottom of all of the muffins is an eggy layer. I’m thinking it might have happened because the rest of the batter was so light as a result of the reaction of the baking soda and the lemon juice? I didn’t add the ingredients in the order you listed and I also hadn’t preheated my oven (it gets hot VERY quickly and things tend to burn when I do preheat it…), just wondering if either of those could have been the reason or if you have any other ideas? I recently found out I am gluten intolerant and your recipes have been such a great resource, thank you for all that you do!


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