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    Home > Recipes > Desserts

    Keto Chocolate Flaxseed Muffins

    portrait of Olivia Wyles
    Author: Olivia Wyles · Updated: Mar 27, 2026
    Pin This! Recipe
    Keto Chocolate Flaxseed Muffins
    Keto Chocolate Flaxseed Muffins
    Keto Chocolate Flaxseed Muffins
    keto chocolate flaxseed muffins in a red silicone baking pan overhead view
    keto chocolate flaxseed muffins Pinterest pin image

    The best part about Valentine's Day is the sweets. And what else says love like breakfast in bed muffins? You don't have to give up your favorites when it comes to holidays. Whip up these decadent Keto Chocolate Flaxseed Muffins for your sweetie!

    Keto Chocolate Flaxseed Muffins in red heart silicone baking pan

    This post may contain affiliate links.

    One of the best memories of Valentine's Day was when my husband placed surprise notes all around the house. Now these weren't handwritten notes. No, these were memes printed out in color. I'm talking Nicolas Cage with a surprised look on his face type memes. With some cute little traditional Valentine's Day quote. Like "Be Mine." It's the little inside jokes that make the best gifts.

    Another great thing he did that Valentine's Day was bake me one of my favorite breakfasts: chocolate muffins. So this year I decided to create a keto version that everyone would love. Even the kids!

    Try my keto carrot cake cupcakes for breakfast too!

    Keto Chocolate Flaxseed Muffins ingredients
    Jump to:
    • Tips for making Keto Chocolate Flaxseed Muffins
    • Keto Flaxseed Muffin Recipe Notes
    • Recipe
    • Comments

    Tips for making Keto Chocolate Flaxseed Muffins

    So my new favorite flour replacement is Flaxseed Meal. It has just the right texture to make delicious allergy-free breakfast muffins. Normally I bake with almond flour. But I wanted this recipe to be completely gluten-free and nut-free without sacrificing flavor. I also wanted to create a breakfast option with all sorts of healthy components. Like omega-3 essential fatty acids and fiber. Flaxseed meal is amazing for that. It's also a natural way to control your cholesterol.

    In this recipe, I use Whole Ground Brown Flaxseed Meal from Bob's Red Mill. I like to use my blender in this because it makes it easier to prep the recipe. And it gives the dry ingredients a nice, smooth texture.

    And I have a new favorite for a Keto approved sweetener: Pyure. Sweetener blends are where it's at. Sometimes I get comments that my Keto baked good dishes have a distinct sharp flavor from the sweetener. So I decided to try out a couple new sweeteners. Organic stevia and erythritol make a great pair in this blend. There is no bitter stevia taste and the erythritol doesn't have that sharp sweet flavor. It's almost like the sweeteners balance each other out.

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    It took me a few tries to get this recipe right, but I think you're going to love the true muffin like texture when these come out of the oven. It pairs well with some sugar-free whipped cream!

    Keto Chocolate Flaxseed Muffins overhead shot in a heart red silicone muffin pan

    More Keto Desserts:

    1. Keto Toasted Almond Shortbread Cookies
    2. Keto Mocha-Espresso Macarons
    3. Keto Red Velvet Brownie Cheesecake
    4. 25 Tasty Quick & Easy Keto Dessert Ideas You'll Actually Make

    Keto Flaxseed Muffin Recipe Notes

    1. You can use any type of Keto approved sweetener, but it may yield different taste results. I just started baking with Pyure, and I found the taste to be very smooth and not too shocking like other Keto sweeteners. Keto sweetener blends are where it's at!
    2. Make sure your eggs and heavy whipping cream are room temperature before baking. It usually takes 30 minutes to 1 hour to get to room temperature. This goes for any Keto baking recipe!
    3. Make sure to melt the butter completely in the microwave, then allow to cool for 2-3 minutes.
    4. If you don't have a fancy blender, that's okay! You might get a more grain-y texture with the flaxseed meal if not blended.
    5. Brown flaxseed meal can be substituted for golden flaxseed meal.
    6. When adding in the flour mixture, just stir the mixture until you don't see any more traces of flour. Don't overmix!
    7. Oven times may vary. Muffins came out perfect for me at 20 minutes in a silicone muffin pan with my gas range.
    8. Cooling time is very important for Keto baking!
    Keto Chocolate Flaxseed Muffins side shot on a white plate, muffin texture

    Try this as a breakfast muffin in a mug recipe -> Keto Flaxseed Muffin in a Mug

    PIN FOR LATER!

    keto chocolate flaxseed muffins in a red silicone baking pan overhead view

    Recipe

    Keto Chocolate Flaxseed Muffins in red heart silicone baking pan side view

    Keto Chocolate Flaxseed Muffins

    4.50 from 100 votes
    Author: Olivia Wyles
    Prep TimePrep: 10 minutes mins
    Cook TimeCook: 20 minutes mins
    Additional Time: 10 minutes mins
    Total TimeTotal: 40 minutes mins
    CourseBreakfast
    CuisineAmerican
    Servings: 6 large muffins
    Print Pin
    Super chocolate-ly and good for you! These Keto Chocolate Flaxseed Muffins are nut-free and flourless which makes them great for a gluten free, low carb, sugar free, and Keto diet. This makes a wonderful healthy breakfast muffin or snack.

    Ingredients

    • ½ cup brown flaxseed meal , finely ground
    • ¼ cup coconut flour
    • 1 tablespoon espresso powder
    • ¼ cup cocoa powder
    • ¼ cup Pyure Organic Stevia Blend*
    • ½ teaspoon salt
    • 2 teaspoons gluten free baking powder
    • 1 teaspoon vanilla extract
    • 4 tablespoons grass-fed butter , melted then cooled
    • ¼ cup avocado oil
    • 2 eggs , room temperature
    • ½ cup heavy whipping cream , room temperature
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    Instructions

    • Gather ingredients and allow eggs and cream to sit out for 30 minutes to 1 hour to get to room temperature.
    • Preheat oven to 325 degrees F and prepare silicone baking muffin pan with paper liners or nonstick cooking spray.
    • In your blender (I recommend Ninja or Vitamix), combine flaxseed meal, coconut flour, espresso powder, cocoa powder, sweetener, salt, and baking powder. Blend on high until the mixture has a fine non-grainy texture. Scrape sides if necessary.
    • In a medium bowl, add butter and melt in the microwave. Allow to cool 2-3 minutes. Add vanilla extract, avocado oil, eggs, and cream and mix well. Add flour mixture and stir until combined. Mixture will be slightly lumpy.
    • Divide batter evenly among prepared muffin cups.
    • Bake 20-25 minutes, until a toothpick inserted in the center comes out clean. Remove from oven and allow to cool at least 10 minutes before removing from pan.

    Notes

    1. You can use any type of keto approved sweetener, but it may yield different taste results.
    2. Make sure your eggs and heavy whipping cream are room temperature before baking.
    3. Melt the butter completely in the microwave, then allow to cool for 2-3 minutes.
    4. Brown flaxseed meal can be substituted for golden flaxseed meal.
    5. Oven times may vary.
    6. Nutrition and carbs – Be aware that some recipe blogs omit sugar alcohols from the nutrition calculation. I have included it and calculated the net carbs. Always use a carb counter app like Cronometer according to the brands you use in order to get accurate nutrition information.
    19.96 Carbs - 6.59 Fiber - 8.35 Sugar Alcohol = 5.03 Net Carbs

    Nutrition

    Serving: 77g | Calories: 304.09kcal (15%) | Carbohydrates: 19.96g (7%) | Protein: 7.14g (14%) | Fat: 26.51g (41%) | Saturated Fat: 9.63g (60%) | Cholesterol: 93.8mg (31%) | Sodium: 195.22mg (8%) | Potassium: 367.19mg (10%) | Fiber: 6.59g (27%) | Sugar: 2.64g (3%) | Net Carbohydrates: 5.03g | Sugar Alcohols: 8.35g
    KEYWORDS: Chocolate Flaxseed Muffins
    Did you love this recipe?I'd love if you'd leave a rating and review below! Your feedback helps others find the recipes more easily! Leave a Review

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    Comments

      4.50 from 100 votes (96 ratings without comment)

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      Recipe Rating




    1. Deb Shirk says

      February 21, 2026 at 9:20 am

      5 stars
      Just came across this recipe. Had all ingredients and wanted to try.....oh my oh my. its the best one out there. I did add 1/4 tsp espresso powder. Texture is the best. I will make often to cure my chocolate cravings.

      Reply
      • Olivia Wyles says

        February 21, 2026 at 4:36 pm

        Oh yay!! Thank you for trying, Deb. I’m so glad you enjoyed 🙂

        Reply
    2. KS says

      July 17, 2024 at 10:21 pm

      5 stars
      These are excellent! Almost identical to the Bread Garden Double Chocolate Keto Muffins from Costco. I doubled the recipe. Great for anyone craving chocolate!

      Reply
      • Olivia Wyles says

        July 18, 2024 at 5:57 am

        Oh wow, thank you for your kind comment and review. I’m glad it turned out great for you!

        Reply
    3. Liv says

      May 22, 2024 at 1:17 am

      Delicious! Just waited the 10mins cooling time after baking as instructed and they are amazing.
      Doubled the batch to make 12 in my regular muffin tray - used a tiny of almond milk to make up to the amount of cream I needed - fabulous, simple, very tasty and not too sweet (used slightly less monkfruit/erythritol sweetener than was suggested).
      Thank you!

      Reply
      • Olivia Wyles says

        May 22, 2024 at 5:55 am

        Excellent! I’m glad they turned out good for you. Great variation ideas 🙂

        Reply
    4. Hibber says

      December 03, 2023 at 7:53 pm

      5 stars
      These are great! I didn’t need to blend the dry ingredients. Just mixed them in a bowl. Substituted half and half for the cream, erythritol for the stevia blend, and coconut oil for the avocado oil and the butter. I added 1T nigella seeds for health benefits and some dried prunes. I would make these again.

      Reply
      • Olivia Wyles says

        December 16, 2023 at 5:49 pm

        Great substitutions! I’m glad they turned out great. Thank you for trying my recipe 🙂

        Reply
    5. Darlene says

      November 07, 2022 at 3:40 pm

      Can I substitute Greek yogurt for the heavy cream?

      Reply
    6. Sue says

      September 19, 2021 at 11:45 am

      I made these and found they were very delicate and crumbled easy. I ended up stirring the whole muffin ( I made 12 smaller ones instead of 6) into my two good vanilla yogurt and it was like cookies and cream!

      Reply
      • Olivia Wyles says

        September 19, 2021 at 11:49 am

        Great idea! When life gives you crumbly muffins, make cookies and cream yogurt. Love it!!

        Reply
    7. Rachel M Kendall says

      April 24, 2021 at 1:16 pm

      Oh man, closest texture to regular bran muffins and so yummy. I added some sf (Erythritol) chocolate chips. They're a very dark chocolate. Which I love! Man oh man with a cup of coffee they're amazing!
      I did have to sub out the avocado oil with vegetable oil because I didn't realize I was out.
      Thanks for the yummy muffin!

      Reply
      • M says

        August 29, 2021 at 2:54 pm

        I made these muffins and while texture was great and moist, they seemed too heavy on the salt. Otherwise great recipe. Next time I will cut back on the salt.

        Reply
      • Deb Shirk says

        February 22, 2026 at 2:48 pm

        4 stars
        I made the mug version yesterday. It was the best I ever had. Made the full recipe here, but then seem very oily to me. Still good, just dont like the oily mouth feel. I will cut back on the avacado oil next time. I also baked them in the oven. I like the darker edges. 350 for aprox 25 min on lower rack.
        thanks for recipe. Do you have other recipes with flax meal..
        I just love that texture and taste.

        Reply
        • Olivia Wyles says

          February 25, 2026 at 10:12 am

          Hi Deb, I have a mug muffin version here that uses butter that might be better! https://oliviawyles.com/keto-flaxseed-muffin-in-a-mug/

          Thank you for your feedback. I don't have many recipes specifically with flax meal, but most of the recipes that use almond flour generally can have flax meal subbed out.

          Reply
    8. susan sell says

      April 11, 2021 at 3:45 am

      Love this recipe, made 12 little muffins, cooked them for 14minutes, and as I didn't have instant coffee I added a tiny restretto! Thank you, lovely muffin texture too.

      Reply
      • Olivia Wyles says

        April 11, 2021 at 8:20 am

        Yay!! I’m so glad to hear they turned out well for you.

        Reply
    picture of Olivia Wyles looking down writing in a book

    Hey, I'm Olivia

    I’m a food creator, mom, picky eater, and cozy gamer with ADHD. I create easy low carb, protein-focused, keto-friendly, sugar-free & gluten-free recipes with minimal ingredients, prep, and dishes. If I can make it, anyone can!

    Learn More

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