
This post may contain affiliate links. Please read my disclosure policy.

About This Recipe
These Lemon Poppy Seed Protein Muffins are seriously sunshine in bite-sized form! They are so fresh, so light, and SO fluffy!
With subtle flavors of lemony goodness and a tender, sink-in-your-teeth texture. They’re the perfect low carb, low calorie breakfast or snack you’ll want to make again and again!
If you like these lemon poppy seed protein muffins you may also enjoy these banana nut protein muffins, skinny blueberry muffins, or double chocolate chip protein muffins!

Why You’ll Love These Lemon Poppyseed Muffins
- Subtly sweet with the perfect light and fluffy texture!
- Low in carbs and calories
- Packed with protein (9g per muffin!)
- A great option for meal prep and freezes great!

Crumble Ingredients
- Sugar – granulated sugar or sugar substitute like Truvia or monk fruit sweetener.
- Butter – cold and cubed small, unsalted or salted
- All-purpose flour – just a little to make the crumble! GF if needed
Muffin Ingredients
- Flour – this recipe calls for coconut flour (which is more more absorbent than other flours) It’s the reason why we’re able to create muffins that are so low in carbs since we’re able to use less of it. It doesn’t have an equal sub, but if you wanted to test with another flour know you’ll probably need 3-4x the amount.
- Protein powder – I used PEScience vanilla. A subtle flavor like cake pop or vanilla works best for this recipe.
- Baking essentials – baking powder, baking soda, xanthan gum (only optional to aide in binding but not necessary), salt and vanilla extract
- Poppy seeds
- Lemon
- Egg
- Coconut oil – or oil of choice. You can also use melted butter.
- Greek yogurt – I used plain Greek yogurt (nonfat, full fat all work). You can also use sour cream.
- Maple syrup – or sugar-free pancake syrup for lower sugar and calories
- Milk – I used almond milk but any milk, dairy or nondairy work!
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 until combined.

6. Add the batter to the 8 muffin cups.

7. Top each muffin with 2 spoonfuls of the crumble. Preheat oven to 425 degrees F. Allow the batter to sit for 10 minutes to increase fluffiness while the oven warms up.

8. Bake for 5 minutes at 425F, then lower to 350F and bake for another 15-20 minutes, or until a toothpick inserted in the center comes out clean.
If you wish to make a glaze, whisk together 1/2 cup powdered sugar, 1 tablespoon fresh lemon juice and 1-2 teaspoons milk until smooth. Drizzle over muffins immediately.
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.
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.
Air Fry For Magic✨
Air frying these muffins for a few minutes gets them slightly crunchy on the outside but still soft and tender on the inside! Just a few minutes at 350F is all you need to get it as golden brown as you’d like

Can I leave out the protein powder?
Sure! I promise, these lemon poppy seed protein muffins do not taste like protein muffins but if you still wish to leave out, I recommend replacing with the same amount of regular flour (not coconut flour since it’s so much more absorbent), you can use all-purpose, gluten-free 1:1 all-purpose 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 3-4 times more absorbent than normal flour (most all flours) and therefore responds differently when baked. This makes it hard to substitute the flour when coconut flour is being used.
If you want to try, I would start with tripling the amount of flour to make up for the extra absorbance properties of coconut flour. Then as more as needed. Note that the muffin batter for this recipe is thicker than your typical muffin batter. See How To Make section above for visuals of what the batter should look like!
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
Dry
- 1/2 cup vanilla protein powder (62g)
- 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 zested
Wet
- 1 large egg
- 1 Tbsp coconut oil (15g) melted
- 1 tsp vanilla extract (5g)
- 1/4 cup plain greek yogurt (60g)
- 1/4 cup maple syrup (60g)
- 2 Tbsp lemon juice (15g) freshly squeezed
- 3/4 cup milk (180g) (I used almond)
Crumble
- 6 Tbsp all-purpose flour (45g) GF if needed
- 1/4 cup sugar (48g) (or substitute)
- 3 Tbsp unsalted butter cold, cut into small cubes
Before You Begin! If you make this, please leave a review and rating letting us know how you liked this recipe! This helps our business thrive & continue providing free recipes. Scroll for macros and MyFitnessPal code.
Instructions
- Make the crumble by combining the flour, sugar and butter in a bowl. Use two forks to cut the butter in. Place in the fridge until needed.
- Add the dry ingredients to a bowl and whisk together.
- In a separate bowl, whisk the egg, coconut oil, and vanilla. Mix in the rest of the wet ingredients.
- Add the dry ingredients to the wet ingredients and fold until just combined.
- Preheat the oven to 425 F. Transfer the batter to the 8 muffin cups. Top each muffin with 2 spoonfuls of the crumble. Allow batter to sit for 10 minutes while oven preheats to increase fluffiness.
- 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.
- If you wish to make a glaze, whisk together 1/2 cup powdered sugar, 1 tablespoon fresh lemon juice and 1-2 teaspoons milk until smooth. Drizzle over muffins immediately.
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.