Keto/Low Carb Lemon Poppyseed Muffins

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Muffins have always been a favorite snack or breakfast. These Keto Lemon Poppyseed Muffins are an excellent substitute for the high-carb variety you often see in stores and are gluten-free. Tons of bright, fresh flavor and only 3 net carbs per muffin in a perfect fit for a low-carb diet.

Keto Lemon poppy seed muffins on a tray with text overlay reading "Lemon poppy seed muffins, keto/low carb"

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Keto/Low Carb Lemon Poppyseed Muffins

I’ve been craving muffins lately. First, I made Keto/Low Carb Mixed Berry Muffins, so I started thinking about other flavors of muffins I love, and Lemon Poppyseed came to mind. Since I had already tweaked the basic muffin recipe, I just needed to experiment with how much lemon zest and lemon juice to add. There is a fine line between the perfect amount and a tad too much.

We ate these Keto/Low Carb Lemon Poppyseed Muffins for breakfast the rest of the week. I warmed them up each morning in the air fryer, then served them with a big slice of butter on top and bacon. My three-year-old woke up asking for more ‘lemony muffins’ this morning, so it looks like it’s time to bake more. Depending on your family size, you may want to double the recipe to make a big batch. This recipe is straightforward and comes together so quickly.

Lemon Poppyseed Muffin Ingredients:

  • Eggs– For this keto muffin recipe, you will need to use six eggs. I promise these Keto Lemon Poppyseed Muffins won’t be eggy. Keto-friendly flours bake very differently than regular gluten-filled flour and require more moisture.
  • Melted Butter– I like to melt my butter in the microwave to make things easy. Cut 9 tbsp of butter and place it into a microwave-safe dish—heat butter at 50% for 60 seconds. Add more time if needed. 
  • cream cheese– My go-to when it comes to cream cheese is Philadelphia cream cheese, but other brands work well too. 
  • Vanilla extract – A little vanilla adds a lot of flavor, so don’t forget to add it.
  • Heavy Whipping Cream–Made from skimming the high-fat cream from dairy milk. Its high-fat content makes it the perfect ingredient for your keto lemon poppyseed muffins.
  • Coconut Flour– This flour is super absorbent, so a little goes a long way. Plus, it adds a little bit of sweetness to your recipe!
  • Salt– A sprinkle of salt helps balance the flavor and bring out the sweetness in your muffins. 
  • Baking Powder– No one likes flat lemon poppy seed muffins! Adding 1 ½ tsp of baking powder will make your muffins look just like the ones in the store.
  • Swerve Granulated– My go-to keto sweetener. Great taste with zero carbs and no sugar.
  • Lemon Zest and Juice– To give your lemon poppyseed muffins some flavor, add lemon zest and lemon juice to the recipe. 

How to Make Keto Lemon Poppyseed Muffins

You can feel free to scroll down to print the keto lemon poppyseed muffin recipe in full. Below, I have included a step-by-step picture tutorial for those who prefer visual tips! Don’t these look delicious?

Keto Lemon Poppy Seed muffins on a plate

Step 1: Preheat the oven to 350. Melt the butter in a large mixing bowl. I like to heat mine in the microwave at 50 percent. Beat eggs together with a whisk.

Six cracked eggs in a clear bowl
Step 2: Add your keto-friendly sweetener. I listed alternatives to Lakanto Monk Fruit Sweetener Classic in the recipe card notes at the bottom of this post.

Keto-friendly sweetener is added to the whisked eggs

Step 3: Mix eggs, sweetener, cream cheese, heavy whipping cream, vanilla, salt, and baking powder until combined.

Cream Cheese is stirred into keto lemon poppy seed muffin mixture

Step 4: Zest and juice two lemons. This keto muffin recipe requires about 1/8th of a cup of lemon juice. Measure out before pouring.

Lemon is zested by citrus zester

Step 5: Add melted butter, coconut flour, lemon zest, lemon juice, and poppyseeds to the muffin mixture and beat again until combined.

Lemon Poppy seed muffin ingredients are mixed together with electric wisk.

Step 6: Pour batter into lined muffin pans in a muffin pan. I’ve been using parchment paper muffin liners I bought on Amazon (here) and loved them! Coconut flour tends to stick to muffin tins. Nothing sticks to parchment paper. 

Keto lemon poppyseed muffin batter in a lined cupcake baking tray.

Step 7: Bake keto lemon poppyseed muffins in a 350-degree oven for 25-30 minutes.

lemon poppyseed muffinThese Keto Lemon Poppyseed Muffins are the perfect low carb treat or breakfast on the go. Ready in minutes, they pack great lemon flavor without guilt!

ENJOY! Serve your keto lemon poppyseed muffins with piping hot butter.


If you have leftover keto lemon poppyseed muffins and want to save them for later, don’t worry, they store well! When storing your keto muffins for short periods, I recommend keeping them in the refrigerator. If fully covered, they should last about a week. Pull them out whenever you’re hungry, for the perfect keto breakfast or pick-me-up snack!

If you want to store muffins for a more extended period, I suggest individually wrapping the muffins in a zip lock bag before placing them in the freezer. They should keep for about six months. 


Yes! In this keto lemon poppyseed muffin recipe, you can use almond flour as a substitute for coconut flour. I choose to use coconut flour due to my daughter’s nuts allergy. Coconut flour is much more absorbent than almond. For every ¼ cup of coconut flour, you need 1 cup of almond flour. This recipe requires 2 cups and 4 tsp of almond flour. 

Note: I have not tested these low carb muffins with almond flour. The substituion is a general substitution. The texture of keto and low carb baked good have aa different texture than muffins made with regular flour.


Not only are these keto lemon poppyseed muffins delicious, but they also have some great health benefits! When it comes to seeds, poppyseeds tend to get overlooked. However, poppy seeds are a great addition to your baked goods, adding crunch and nutritional value. Did you know one teaspoon of poppy seeds has enough calcium and phosphorus to meet 4% of your recommended daily intake, 2-3% of your zinc, and 2-4% of your iron intake? These nutrients help your body create strong bones, cells, and a healthy immune system.

Keto Lemon Poppyseed Muffins 15

Keto Lifestyle Tips and Resources

If you are new to the keto lifestyle, you know it can be overwhelming. Check out our page for Easy Keto/Low Carb Recipes on Facebook. I post all my new recipes here. If you enjoy Pinterest I’d love if you’d follow me here. You may also want to check out our Guide to Getting Started with Keto for many excellent tips and links to my favorite resources.

If you are just getting started following a keto diet and want more information, there are tons of fantastic resources. Amazon has several great books you may want to check out here.

More Keto Bread Recipes

If you enjoyed these keto lemon poppyseed muffins, check out these other muffin variations. They are sure to please!

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4.54 from 26 votes

Keto/Low Carb Poppy Seed Muffins

Muffins have always been a favorite snack or breakfast. These Keto Lemon Poppyseed Muffins are a great substitute for the high carb variety you often see in stores. Tons of bright fresh flavor and low in carbs means it fits into your daily macros with ease!
Prep Time10 minutes
Cook Time25 minutes
Total Time35 minutes
Course: Breakfast, Dessert, Snack
Cuisine: American
Keyword: Lemon Poppyseed Muffins
Servings: 16
Calories: 109kcal
Author: Kasey Trenum



  • Preheat oven to 350. 
  • Melt butter.
  • Beat eggs, Lakanto Monkfruit, cream cheese, heavy whipping cream, vanilla, salt, and baking powder until combined. 
  • Add melted butter, coconut flour, lemon zest, lemon juice, and poppy seeds to the mixture and beat again until combined.
  • Pour batter into lined muffin pans. I've been using parchment paper muffin liners I bought on Amazon (here) and loved them! 
  • Bake for 25-30 minutes or until the tops are just beginning to brown and a toothpick inserted in the center comes out clean. 


Calories: 109kcal | Carbohydrates: 5g | Protein: 3g | Fat: 9g | Saturated Fat: 5g | Cholesterol: 81mg | Sodium: 176mg | Potassium: 97mg | Fiber: 2g | Vitamin A: 315IU | Vitamin C: 8mg | Calcium: 44mg | Iron: 0.4mg
Tried this recipe?Mention @kaseytrenumblogger or tag #kaseytrenumblogger!


  1. these look yummy…..I have two questions …These are miniature muffins right?……..Is one portion 2 muffins or 1?

    1. They are standard sized muffins. The nutritional info is per muffin so each person could determine their own servings size.

    2. 5 stars
      In an old recipe of my grandmother’s poppyseed cake instead of using your cream cheese warned in microwave, use sour cream and baking soda. So I LL play around with it but in thinking 1/2 C of sour cream mixed with 1 teaspoon of baking soda will work and taste amazing.. make sure you mix those two first then alternately add as you mix.

    3. PS. Do not melt your butter get it to room temperature than mix. Trust me. Makes a world of a difference and taste.

  2. How do you measure the butter – I’m so used to 1/4 cup, 1/2 cup measurement sizes? So do I melt butter then measure out the tbsps or measure tbsps then melt?

  3. So good! I made 12 larger muffins. So light and refreshing! Next time I think I’ll add another Tbl of lemon juice for even more lemon flavor! Thanks, Kasey! Adding to breakfast line up.

  4. Hi Kasey, I’ve been on Keto now for 6 weeks and lost 5kg which I’m happy about, but have been struggling for recipes. Now having found your site I’m going to try some new changes as hubby is getting sick of as they say “meat and 2 vegies” being cabbage or cauliflower with either mushrooms or tomatoes. My query though is what can I use in place of Swerve and Monkfruit sweetener as we don’t have these products here in Australia. I’ve even been having trouble to find Xanthan and Erythritol, but can purchase Stevia.

    1. Hi Josephine,

      So glad my recipes have been helpful. I am not sure what products are available in Australia to be able to make a suggestion.

    2. Xanthan gum is in many supermarkets in Qld as is Natvia and monk fruit sweetness. I also buy erythritol in an organic health superstore. I am sure you could google suppliers in your area – good luck

    3. Hey! A bit late to the party, but I’m in Australia. I usually substitute Swerve for Stevia 1:1. Personally my favourite is Natvia.

      Xanthan is usually in the baking isle. If you have trouble then ask some one who works there to help.

    4. I’m in south east Queensland and my local Coles store has xanthum gum in health food isle. You can also buy monk fruit and stevia at supermarkets now. Xylitol and erythrotol are still only at healthfood shops as far as I know

  5. These were delicious! Perfect lemon flavor, and love that they are made with coconut flour. I can see myself making these on a regular basis. Thank you so much!

  6. Do these freeze well?? Its just my husband and myself, and I don’t want to have to eat ALL the muffins at once… so it would be amazing if I could freeze some and pull them out and pop them in the microwave for a bit.

    1. I haven’t frozen them but have heard from others who said they did and they froze well.

    1. I haven’t tested it with almond flour because my daught4er is allergic to almonds. But if you do, you would need 4x as much almond flour as it is not a 1:1 substitution.

  7. Hi Kasey. Do you prefer coconut flour over almond flour? What’s the measurement difference between the two? I know it’s not 1 for 1 thx

    1. I use coconut flour because my oldest daughter is allergic to almonds. 1/4 coconut flour is equal to 1 cup almond flour.

  8. This recipe is amazing. I’ve made it so many times since I found it! The perks of having a well established lemon tree. My kids love it for breakfast or a sneaky lunchbox treat. Hubby loves it for dessert. I love it for a filling grab and go meal.

    I’ve made it a couple of different ways:
    24 cup mini muffin tray – makes 2 trays (if you don’t eat the batter). Bake for 12-13 mins.
    25cm square cake pan – I cut it into 21 pieces. Baked at 350 (190°C) for 25 mins, but next time will try the cooking temp and time from your lemon bread recipe.

    I’m planning on trying this with orange zest and juice when my oranges ripen in August. I’ll let you onow how it goes.

  9. I enjoy lemon poppy seed but prefer almond poppy seed. I’m not a baker so I don’t know how substitutuons would work, but do you think there would be a way to sub almond extract for the lemon juice/zest? I know you don’t cook with almonds because of your daughter’s allergy, just curious if you know a good ratio/sub using extracts because they are stronger than the real thing. Thanks!

    1. I sure don’t. Just don’t know how the conversion rate would work. You may just have to play with it an see. Hope you can figure it out!!

4.54 from 26 votes (21 ratings without comment)

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