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About This Recipe
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!
Want more healthy and delicious muffins? Try my infamous Light and Fluffy Skinny Blueberry Muffins! You also can’t go wrong with my Banana Nut Protein Muffins with Pecan Crumble or my Double Chocolate Chip Protein Muffins!

Why You’ll Love These Lemon Poppyseed Muffins
- 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!

- Sugar – granulated sugar or sweetener of choice
- Flour – I used all-purpose and coconut flour. Use gluten-free flour if needed. My favorites are Bob’s Red Mill 1:1 and King Arthur’s Measure for Measure
- Butter
- Protein powder – I used PEScience Vanilla. 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.
- Baking essentials: baking powder, baking soda, xanthan gum (optional), salt, vanilla extract.
- Poppy seeds
- Lemon
- Egg
- Coconut oil – or oil of choice
- Greek yogurt – I used nonfat plain Greek yogurt
- Maple syrup – can also use sugar-free pancake syrup
- Milk – I used almond milk but any milk of choice works
How To Make
The full printable recipe is below, but let me walk you through the process so you know what to expect when you’re making it!

1. For the Crumb Topping: combine the sugar, flour and butter in a large bowl using two forks or a pastry cutter.

2. You want a crumbly mixture and the crumbs should be pea-sized. Place mixture in the fridge or freezer until needed.

3. For the Muffins: Preheat the oven to 425 F. Line 8 muffin cups with cupcake liners. Add the dry ingredients to a bowl and whisk the dry ingredients together.

4. In a separate small bowl, whisk the egg, coconut oil, and vanilla. Then stir in the rest of the wet ingredients.

5. Add the dry ingredients to the wet ingredients and fold just until combined. Do not over-mix (this keeps the muffins fluffy). Allow the batter to sit for 10 minutes, which also helps with fluffiness.

6. Add the batter to the 8 muffin cups.

7. Top each muffin with 2 spoonfuls of the crumble.

8. Bake for 5 minutes at 425 F, then lower to 350 F while the muffins are still in the oven and bake for another 15-20 minutes, or until a toothpick inserted in the center comes out clean.
Optional glaze: In a small bowl combine the confectioners’ sugar, lemon extract, lemon juice, and milk; whisk until smooth, adding more milk as needed to reach desired consistency. Drizzle over the muffins right before serving.
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.
Helpful Tips
- 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.

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.
More Muffin Recipes You’ll Love
Did you make this? If you snap a photo, please be sure leave a review, tag me on Instagram or TikTok at @LaurenFitFoodie or hashtag #LaurenFitFoodie so I can see your creations!

Low Carb Lemon Poppy Seed Protein Muffins
Ingredients
Crumble:
- 1/4 cup granulated sugar or sweetener
- 6 Tbsp all-purpose flour use gluten-free if needed
- 3 Tbsp unsalted butter chilled and cut into tiny pieces
Muffins (Dry Ingredients):
- 1/2 cup vanilla protein powder (62)
- 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
- 1 medium lemon the zest of
Muffins (Wet Ingredients):
- 1 large egg
- 1 Tbsp coconut oil (15g) melted
- 1 tsp vanilla extract (5g)
- 1/4 cup plain nonfat greek yogurt (60g)
- 1/4 cup maple syrup (60g)
- 2 Tbsp lemon juice (15g) freshly squeezed
- 3/4 cup unsweetened almond milk (180g) or milk of choice
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Instructions
For the Crumb Topping:
- Combine the sugar, flour and butter in a large bowl using two forks or a pastry cutter. You want a crumbly mixture and the crumbs should be pea-sized. Place mixture in the fridge or freezer until needed.
For the Muffins:
- Preheat the oven to 425 F. Line 8 muffin cups with cupcake liners.
- Add the dry ingredients to a bowl and whisk the dry ingredients together.
- In a separate small bowl, whisk the egg, coconut oil, and vanilla. Then stir in the rest of the wet ingredients.
- Add the dry ingredients to the wet ingredients and fold just until combined. Do not over-mix (this keeps the muffins fluffy). Allow the batter to sit for 10 minutes, which also helps with fluffiness.
- Add the batter to the 8 muffin cups. Top each muffin with 2 spoonfuls of the crumble.
- Bake for 5 minutes at 425 F, then lower to 350 F while the muffins are still in the oven and bake for another 15-20 minutes, or until a toothpick inserted in the center comes out clean.
Optional Glaze:
- In a small bowl, combine the confectioner's sugar, lemon extract, lemon juice and milk; wish until smooth, adding more milk as needed to reach desired consistency. Drizzle over the muffins right before serving.
Equipment
Notes
Nutrition Information
Nutrition is hand-calculated and accurate. No autocalulations! However, note that values can vary based on the brands you use and if you substitute ingredients.