This quick and easy recipe for Low-Carb Lemon Poppy Seed Muffins starts your day on a bright note. These tender muffins boast the traditional flavor combination of lemon and poppy seeds. These muffins can be part of a low-carb, keto, Paleo, dairy-free, gluten-free, or diabetic diet.


Lemon-Poppy-Seed-Muffins-buttered and ready for eating.


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The recipe

These muffins are loaded with citrus flavor and sure to start your day on a bright happy note. Poppy seeds add hints reminiscent of Earl Grey tea and they also give a bit of texture to the muffins. 


I like breaking open the steaming hot muffins and slathering butter on each half. If you don’t eat butter, no problem. You may want to spread on this low-carb strawberry jam from Sugar Free Londoner instead. 


Lemon-Poppy-Seed-Muffins-Cloase-up of buttered muffin


Short on time? This recipe is for you! The pre-prep it requires is zesting and juicing the lemon.


Lemon-Poppy-Seed-Muffins-zesting the lemon.


The rest is just mixing the dry ingredients together, then whisking the wet ingredients. Next you stir the wet ingredients into the dry, then fill up the muffin cups and pop them in the oven. So easy!


Lemon-Poppy-Seed-Muffins-dry ingredients


The inspiration 

This recipe was inspired by those huge lemon poppy seed muffins we see in coffee shops everywhere. You know the ones. They sit in the pastry display along with the other pastries tantalizing you as you order that low-carb coffee. 


I wanted to make a muffin that’s just as tasty as the coffee shop variety, but with fewer carbs so we can enjoy them without the guilt. 


Lemon-Poppy-Seed-Muffins-staying warm in a towel.


Because I get a lot of questions about substituting coconut flour for almond flour recipes, I realized that many of my followers prefer coconut flour, so I decided to branch out of my baking comfort zone and make them with coconut flour. 


In developing this recipe, I altered one of my very early recipes on the website, Paleo Lemon Poppyseed Jar Cakes


Lemon-Poppy-Seed-Muffins-in the tin with lemons and coffee pot behind.


Is coconut a nut?

One reason why I chose to use coconut flour in this recipe is because so many people have nut allergies. I have been getting loads of requests for nut-free recipes.


The FDA classifies the coconut as a tree nut. In fact, the Food Allergen Labeling and Consumer Protection Act requires it be listed on food labels as a tree nut.


Biologically, the coconut is actually the seed of a drupaceous fruit. Drupes are more commonly called stone fruits and include peaches and nectarines.


Many people with tree nut allergies can safely eat coconut, but if you have a tree nut allergy, you should talk to your allergy physician before trying coconut products.


Some people do have allergies and sensitivities to coconut. In fact, my daughter has a sensitivity to coconut, so I haven’t used it in a lot of recipes. Now that she’s in college, I plan to branch out a bit more.


Coconut Flour VS Almond Flour

Using coconut flour in recipes is a little different than using almond flour. It has a slightly different texture, a different flavor, and different absorption qualities.


I find that the texture of coconut flour is slightly more fibrous than almond flour. It gives baked goods a different texture than almond flour–maybe a little fluffier. 


Coconut flour does give baked goods a slight tropical, coconut flavor. I find it pleasant and enjoy it, but if you don’t like coconut, coconut flour may not be right for you. 


Finally, coconut flour absorbs liquid like you wouldn’t believe! When you first add the wet ingredients, it looks like the batter is going to be too runny. Don’t worry about that. In a few minutes, all that extra liquid will be sucked up by the coconut flour.


Because of the ability of coconut flour to absorb liquids, you don’t need to use nearly as much flour. This makes it a bit less expensive.


Also, note that almond flour and coconut flour are not interchangeable in the same quantity in recipes. Not only the quantity of flour needed will be different, but the amount of liquid will change as well. If you’d like more information, check out this article on coconut flour vs. almond flour.


Lemon-Poppy-Seed-Muffins-wet ingredients.


How to store muffins

Should you not eat all of the muffins in one sitting, no worries. You can store them for later. 


To store the muffins, first be sure that they are completely cooled. Next, line an airtight container with a paper towel. The paper towel absorbs any moisture that comes out of the muffins and keeps them from getting soggy.


Place the muffins in a single layer in the container and cover them with another paper towel on top before putting on the lid. 


The USDA says that muffins are shelf stable and do not require refrigeration. Of course, if they show signs of mold or smell funny, don’t eat them. I keep them at room temperature for up to 3 days. If I’m not going to use them within 3 days, I put them in the freezer.


To freeze them, put them in a single layer in an air-tight container. If you want to use them one-by-one, you can put them in multiple small containers, like half-pint freezer safe jars. 


When you’re ready to eat, allow them to defrost at room temperature. They taste even better when you reheat them before eating.


Final words

These muffins are so easy to make and nice to have in the freezer for a quick grab-n-go snack. They may be low-carb and gluten-free, but they are every bit as good as those muffins you see in the coffee shop.

Love lemon and need other low-carb lemon recipes? Check out our Keto Easy Lemon Chia Pudding Recipe, our Low-Carb Lemon Danish Pastries, or this keto lemon cheesecake from Joy Filled Eats. Enjoy!



Lemon Poppy Seed Muffins recipe

This recipe for Low-Carb Lemon Poppy Seed Muffins is for my lemon lovers! Be sure to let you lemon-loving friends know about this one! ❤️🍋

Lemon-Poppy-Seed-Muffins-Fresh from the oven.
4.91 from 10 votes

Low-Carb Lemon Poppy Seed Muffins Recipe (Paleo and Keto-Friendly)

This quick and easy recipe for Low-Carb Lemon Poppy Seed Muffins starts your day on a bright note. These tender muffins boast the traditional flavor combination of lemon and poppy seeds. These muffins can be part of a low-carb, keto, Paleo, dairy-free, gluten-free, or diabetic diet.

Course Breakfast, Snack
Cuisine American
Keyword dairy-free, gluten-free, keto poppy seed muffins, lemon poppy seed muffins, low carb lemon poppy seed muffins, paleo poppy seed muffins
Prep Time 8 minutes
Cook Time 22 minutes
Total Time 30 minutes
Servings 12
Calories 118 kcal
Author Annissa Slusher



  1. Preheat oven to 350º Fahrenheit. Line a 12 cup muffin pan with paper liners.

  2. In a medium mixing bowl whisk together the coconut flour, sweetener, baking soda, poppy seeds and lemon zest. 

    Lemon-Poppy-Seed-Muffins-dry ingredients.
  3. Whisk together the almond milk, avocado oil., eggs, and lemon juice in a separate mixing bowl. 

    Lemon-Poppy-Seed-Muffins-wet ingredients.
  4. Pour the wet ingredient mixture into the dry ingredients and stir to blend. Spoon mixture into the prepared muffin pan, distributing it equally among the muffin cups. 

  5. Bake for 20-23 minutes, or until the tops spring back when lightly touched or a toothpick inserted int the middle of the muffins comes out clean. Serve warm.

    Lemon-Poppy-Seed-Muffins-Fresh from the oven.
Nutrition Facts
Low-Carb Lemon Poppy Seed Muffins Recipe (Paleo and Keto-Friendly)
Amount Per Serving (1 muffin)
Calories 118 Calories from Fat 81
% Daily Value*
Fat 9g14%
Saturated Fat 2g13%
Trans Fat 0g
Polyunsaturated Fat 2g
Monounsaturated Fat 5g
Cholesterol 62mg21%
Sodium 95mg4%
Potassium 41mg1%
Carbohydrates 5g2%
Fiber 3g13%
Sugar 1g1%
Protein 3g6%
Vitamin A 100%2%
Vitamin C 3.3%4%
Calcium 40%4%
Iron 1.4%8%
* Percent Daily Values are based on a 2000 calorie diet.