Some days you just need a little low-carb treat without the guilt, enter our Keto Lemon Poppy Seed Muffins recipe, they’re very tasty, moist, and never dry.

These low-carb muffins are fluffy and moist with a subtle citrus zing; the lemon frosting takes this humble keto snack to a whole new level.
Want more cupcakes? Head over to our Ultimate Low Carb Cupcake Recipe for the perfect chocolate and vanilla cupcake.
Keto Lemon Poppy Seed Muffins Ingredients
- Muffin Ingredients
- 2 cups of Almond Flour
- 2 teaspoons of Baking Powder
- 1/3 cup of Erythritol (regular granulated)
- 2 Eggs
- 1 cup of Sour Cream
- 1 teaspoon of Vanilla Extract
- 1 tablespoon of Poppy Seeds
- 1 Lemon, zest, and juice
- Lemon Frosting Ingredients
- 4 ounces of Unsalted Butter, softened
- 1 tablespoon of Lemon Juice
- 1/2 cup of Powdered Erythritol
- 2 tablespoons of Heavy Cream
How To Make Keto Lemon Poppy Seed Muffins

- Preheat oven to 180C/355F.
- Place all cupcake ingredients into your stand mixer and mix on medium for 3 minutes, until combined.
- Spoon the mixture into 12 holes of a muffin tin, lined with cupcake papers. Fill each paper ¾ full.
- Bake for 20-25 minutes, until a skewer, comes out clean when inserted in the center.
- Cool the cupcakes on a cake rack.
- While the cupcakes are cooling, place the butter and lemon juice in your stand mixer.
- Mix on low whilst adding the Powdered Erythritol by the spoonful. Add the cream.
- Mix on medium until the ingredients are fluffy and pale.
- Gently spoon the mixture into a piping bag and pipe onto your cooled cupcakes. Enjoy!

Keto Lemon Poppy Seed Muffins (3g Carbs)
Unit Conversion
Ingredients
Cupcake
- 2 cups Almond Flour
- 2 teaspoons Baking Powder
- 1/3 cup Erythritol normal granulated not powdered
- 2 large Eggs
- 1 cup Sour Cream
- 1 teaspoon Vanilla Extract
- 1 tablespoon Poppy Seeds
- 1 Lemon zest and juice
Frosting
- 4 ounces Unsalted Butter unsalted
- 1 tablespoon Lemon Juice
- 1/2 cup Powdered Erythritol
- 2 tablespoons Heavy Cream
Instructions
- Preheat oven to 180C/355F.
- Place all cupcake ingredients into your stand mixer and mix on medium for 3 minutes, until combined.
- Spoon the mixture into 12 holes of a muffin tin, lined with cupcake papers. Fill each paper ¾ full.
- Bake for 20-25 minutes, until a skewer comes out clean when inserted in the center.
- Cool the cupcakes on a cake rack.
- While the cupcakes are cooling, place the butter and lemon juice in your stand mixer.
- Mix on low whilst adding the Natvia Icing Mix by the spoonful. Add the cream.
- Mix on medium until the ingredients fluffy and pale.
- Gently spoon the mixture into a piping bag and pipe onto your cooled cupcakes. Enjoy!
Notes
Nutrition

How To Store Lemon Poppy Seed Muffins
Store lemon poppy seed muffins in the fridge for up to 5 days in a plastic container, they are not suitable for freezing.
Our muffins and cupcakes recipes (and other baked goods) are made ketogenic due to our use of select low-carb keto flour substitutes.
If you like these lemon and poppyseed cupcakes; try our;
To make a larger batch of this Low Carb Lemon Poppy Seed Keto Muffins recipe, adjust the servings in the recipe card above.
Made this today and it’s amazing! My husband and I loved it, will definitely make it again 🙂
I’m so glad that you and your husband enjoyed them!!
Those look delicious!
These were just AMAZING! It’s a keeper for sure!
I used sesame flour instead of almond and also crushed my poppy seeds to bring out the flavor, my dough was so thick and when they were baked the dough did not loosen any and came out the same clumpy shape as when I put them in, not sure if the crushed poppy seed sucked up moister but recipe was a fail.
Hi Shannon,
Changing the flour and crushing the poppy seeds are 100% the reason why the recipe failed. If you want the cupcakes to come out successfully, I would recommend following the recipe exactly.
Can I use chia seeds instead of poppy seeds? Will that be a 1:1 substitution?
Thanks!
Hi Zeytin,
I don’t recommend using chia seeds for this recipe as they react differently to poppy seeds and will change the texture of the cake.
Just finished making these and they are so delishious!if I only use erythritol does that bring the carb count down?
Hi Mary,
Glad you like them! Natvia is pretty similar to plain erythritol, it wouldn’t make a noticeable difference to the carb count.
What’s Natvia?
Hi Melissa,
Natvia is a sweetener that is a blend of erythritol and stevia.
I love poppy seeds! I’m gonna try this very soon. Perfect is, that we are major producers of poppy seeds, so it is very cheep here in central Europe. About 4-6 dollars for 1kg (aprox. 2.2 pounds)..:-) We also make desserts only with poppy seeds, eggs, butter, little bit of lemon and sugar substitutes. Yummy…
We love them too Petra! Thanks for dropping by.
Very yummy! Is it really 366 calories for one little cupcake? I love them so much I want more, but hesitate with tha calorie count!
I make these all the time now, they are amazing. Yesterday I added raspberry extract and now they are like a raspberry lemonade, so yummy. I changed the frosting to cream cheese rather than butter and I add more poopy seeds. I use swerve as my sugar. I’m going to keep changing up the flavors to see what else is tasty, I was thinking of trying a banana extract with some nuts instead next time.
Hi Michael,
What a great flavor combination. Raspberry Lemonade sounds divine! Thank you for your kind words 🙂
Would I be able to substitute lemon zest for almond extract to get something closer to the poppy seed muffins that aren’t lemon? Or is the zest somehow part of the structural integrity of the muffin? (Like, does the citrus cause a reaction to help them rise or something like that)
Hi Brittany,
The lemon zest is purely included for flavor and substituting will not affect the structure. I’d love to hear how almond ones turn out!
If I wanted to make in a loaf pan, how long would you recommend to bake? Also if I only have powdery/granular sweetener do you think that would be ok for the frosting or do I need to seek out icing style?
Hi Kim,
I would recommend seeking out a powered or confectioners sweetener for the frosting as granulated sweetener won’t dissolve
For a loaf pan, I would recommend dropping the temperature to 170C/340F and baking for 30 minutes to start with and monitor closely until it is cooked through. I estimate that it would take 50 minutes to cook through, but it’s better to keep an eye on it and have it turn out perfect. Let us know how it goes.
Gerri
Have you used any other sweeteners successfully?
Hi Chelly,
We use either xylitol, liquid stevia, erythritol or Natvia (erythritol and stevia blend) interchangeably in each recipe. Just beware that both liquid stevia and xylitol are sweeter than the others and xylitol is also toxic to pets. I hope that answers your question.
Gerri
I made these with granular and powdered erythritol and they were so good! Very lemony and zesty, next time I may even add more poppy seeds and lemon zest.
Hi Jennifer,
Thank you for your kind words. I’m glad you liked them
Gerri