Holding a lemon poppy protein seed muffin

Low Carb Lemon Poppy Seed Protein Muffins

These Low Carb Lemon Poppy Seed Protein Muffins are so fresh, light, and fluffy! With wholesome ingredients, subtle flavors of lemony goodness and a moist, melt in your mouth texture, they’re the perfect low calorie lighter breakfast or snack you’ll want to make again and again.

One of my favorite flavors of the summer is lemon! Not only does it smell so refreshing and bright, but it has the most invigorating and lively taste. It’s one of those flavors that just makes you feel so good—and I mean that. Snacking on something lemony gets my day off to a great start, and it’s turned some bad days around, too!

My mom has been begging me to make a lemon recipe for a few weeks now, and with summer officially here, I thought this would be the perfect time to share with you my Lemon Poppy Seed Protein Muffins. They are SO fresh, SO light, and SO fluffy! With wholesome ingredients, subtle flavors of lemony goodness and a moist, melt in your mouth texture, they’re the perfect low carb, low calorie breakfast or snack you’ll want to make again and again.

They’re seriously sunshine in bite-sized form!


  • Perfectly light and fluffy texture.
  • Subtly sweet, tangy, and amazingly refreshing!
  • Made with wholesome, fresh ingredients.
  • Low carb, low calorie, and packed with protein!
  • A great option for meal prep.
  • So easy & simple to make!


  • Protein Powder – I used PEScience Cake Pop. A subtle flavor like cake pop or vanilla works best for this recipe. If you want to use another protein powder, just make sure it is one that is a whey + casein blend. For all Pescience products, you can use my affiliate code LaurenFitFoodie to save 10% off your purchase.
  • Coconut flour – unfortunately coconut flour is the one flour that is hardest to substitute. This is because it is so much more absorbent than all other flours. I haven’t tried personally, but if you wanted to sub, I would recommend starting with 2x the amount of all-purpose or oat flour, and you may need to increase to 3-4x the amount. If anyone tries it with another flour, let us know in the comments!
  • Lemon – Use the juice and zest for that fresh lemon flavor!
  • Coconut oil – or any oil of choice.
  • Egg
  • Greek yogurt – I used plain Greek yogurt for these muffins.
  • Syrup – To keep this recipe lighter, I used sugar-free pancake syrup but feel free to use pure maple syrup or honey!
  • Classic baking goods – You’ll need baking powder, baking soda, salt, and vanilla extract.
  • Xanthum gum – Optional to hold the muffins together better. I use Bob Red Mill.
  • Milk – I used unsweetened vanilla almond milk. Any milk works though!


No fancy equipment is required to make these Lemon Poppy Seed Protein Muffins! All you need are some old fashioned mixing bowls, a muffin pan, a whisk, and a spoon.

Follow these easy steps:

  • First, dry ingredients. Combine the coconut flour, lemon zest, baking powder, baking soda, xanthum gum, salt, and sweetener. Then, stir in the protein powder. Use a larger bowl for this since this is where you’ll be mixing the final batter.
  • Then, wet ingredients. Whisk together the melted coconut oil, egg, and vanilla. Stir in the lemon juice, syrup, yogurt, and almond milk.
  • Give it a quick mix. Combine your wet and dry ingredients. The less vigorously you mix, the fluffier your muffins will be!
  • Bake. Pour batter in muffin pan and bake for 20-25 minutes!


  • Protein powder: These muffins use a whey + casein blend protein powder, so make sure whatever brand you plan to substitute is also a whey + casein blend and a brand that bakes well. I only have experience baking with PEScience protein powders, so I can’t vouch for other brands. However, I do know some bake better than others. I’d also recommend a neutral flavor so it doesn’t overpower the lemon in the muffins. If you wish to omit the protein powder completely, just do so gram for gram with all-purpose, whole wheat, oat, or gluten-free flour.
  • Coconut flour: Coconut flour is about 3 times as absorbent as regular flour, so I wouldn’t recommend replacing with another flour if you can help it. If you must, I recommend using all-purpose, whole wheat, oat, or gluten-free flour and tripling the amount. This will change the nutritional information.
  • Coconut oil: You can substitute with canola oil or butter. You could also use olive oil. Note that it would bring a stronger olive oil flavor to the muffins.
  • Syrup: I used sugar-free pancake syrup to keep the calories a little lower. Normal pancake syrup, maple syrup, agave, honey, or any other sticky sweetener would work!
  • Milk: Almond, cashew, dairy…any milk of choice works here!


  • Organize and prepare! Always read the recipe first and make sure you have all the ingredients, that they’re at the right temperatures, and that you have the proper equipment and space to make it. This will make the process so much easier!
  • Use a silicone muffin pan. Silicone makes baking a breeze! No more losing half your muffin in aluminum pans or liners. Barely any clean up!
  • Don’t over mix! Really! Over mixing can really mess up the texture.


Keep your muffins stored in an airtight container or Ziploc bag in the fridge for up to a week. Or you can leave out and they will stay fresh for about 5 days. I prefer them fresh out of the fridge; Simon likes them best at room temp.

If freezing, wrap each muffin individually in aluminum foil, plastic wrap, or parchment paper and keep stored in an airtight Ziploc bag. Sealing air tight prevents freezer burn. Let defrost overnight in the fridge.


Can I leave out the protein powder?

I promise, these do not taste like protein muffins at all. But if you still wish to leave out, I would replace with the same amount of flour (use all-purpose, gluten-free 1:1 all-purpose, oat, or whole wheat flour) so that a similar balance of wet and dry ingredients is achieved.

How do I make my muffins light and fluffy?

Don’t beat the batter. Just mix well. This is why I recommend using a whisk to combine the ingredients and not a hand mixer. Over-mixing will create dry muffins.

Allowing the batter to sit for 10 minutes before baking also creates a fluffier texture. The extra time allows the ingredients to come together more effectively.

Can I use another flour instead of coconut flour?

Coconut flour is about 3 times more absorbent than normal flour, and therefore responds differently when baked. So I wouldn’t if you can help it!

But if you must, I would 2-4x the amount of the flour you use to make up for the extra absorbance properties of coconut flour.


Love muffins as much as I do? Check out some of these other delicious recipes 😋





If you try these Lemon Poppy Seed Protein Muffins and love them, please rate this recipe!

You can also tag me on Instagram, @LaurenFitFoodie. It makes my day seeing your yummy recreations!

Yield: 8

Low Carb Lemon Poppy Seed Protein Muffins

Holding a lemon poppy protein seed muffin

These muffins are so fresh, light, and fluffy! They taste like sunshine in bite-size form and they're the perfect low carb, low calorie breakfast or snack you'll want to make again and again!

Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes


  • 2 scoops Cake Pop or Vanilla protein powder (62g) - I used PEScience Cake Pop
  • 1/2 cup coconut flour (56g)
  • 1/2 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 tsp xanthan gum (2g), optional for binding
  • 1/4 tsp salt
  • 1 Tbsp poppy seeds (8g)
  • 1 tbsp lemon zest (14g), about 1 medium lemon
  • 1 large egg
  • 1 Tbsp coconut oil, melted(15g)
  • 1 tsp vanilla extract (5g)
  • 1/4 cup plain nonfat Greek yogurt (60g) - Use dairy-free if needed.
  • 1/4 cup sugar-free pancake syrup (60g)
  • 2 Tbsp fresh lemon juice (15g), about one medium lemon
  • 3/4 cup unsweetened almond milk (180g)


  1. Preheat the oven to 350 F. Spray 8 muffin cups with cooking spray. I recommend using a silicone muffin pan if possible, or otherwise, liners may be useful.
  2. Add the protein powder, coconut flour, baking powder, baking soda, xanthan gum, salt, poppy seeds and lemon zest to a bowl. Whisk the dry ingredients together.
  3. In a separate small bowl, whisk the egg, melted coconut oil, and vanilla. Then stir in the yogurt, pancake syrup, lemon juice, and almond milk. Mix until well combined.
  4. Add the dry ingredients to the wet ingredients and fold until combined. Do not over-mix (this keeps the muffins fluffy). Allow the batter to sit for 10 minutes, which also helps with fluffiness.
  5. Add the batter to the 8 muffin cups. Bake at 350 F. for 20-25 minutes, or until toothpick inserted in center comes out clean.


MFP entry: LFF Lemon Poppy Seed Protein Muffins

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    Nutrition Information:



    Serving Size:

    1 muffin (55g)

    Amount Per Serving: Calories: 94Total Fat: 3.8gSaturated Fat: 2.6gCarbohydrates: 5.7gFiber: 2.6gSugar: 0.7gProtein: 8.6g

    Did you make this recipe?

    Please leave a comment on the blog or share a photo on Instagram and tag me @LaurenFitFoodie! 


        • Hi Lauren, can you use another liquid other than a milk product? Water, apple sauce, light lemonade etc?

          • Hey Nicole, I haven’t tried it myself, but I don’t see why another liquid like water or lemonade wouldn’t work! If you try it, I would love to hear how it turns out! 😊

    1. I haven’t left a comment before but all your recipes I’ve tried are amazing! I’d been looking for a baking recipe with the only flour being coconut flour, instead of a combo of multiple like so many are!
      I made these a few days ago, per recipe besides an extra 1 tbsp of poppy seeds for some more healthy fats, and a teaspoon of lemon extract! Thank you so much, you’re a recipe genius!!

      • Adoree,

        Thank you so much for taking the time to leave this review! I am grinning from ear to ear reading it!😊 So glad you loved them! And just love the additions you added!

    2. I was SO excited for this recipe and it didn’t disappoint. I ended up with 11 muffins and they are amazing. The perfect amount of bright lemon flavor and lovely texture. There are endless possibilities and I think I’m going to try orange poppyseed next!

      • Thank you for your sweet commment Hallie! I am so happy to hear you loved them. OMG orange poppyseed?! Now we are talking 😍

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