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4.90 from 19 votes
Home By Course Breakfast Muffins & Breads

Lemon Poppy Seed Protein Muffins (low carb)

These Low Carb Lemon Poppy Seed Protein 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!

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By: Lauren published: Jun. 10, 2021 updated: Aug. 11, 2024 17 Comments

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Lemon poppyseed protein muffins on a plate.
Contents hide
About This Recipe
Why You’ll Love These Lemon Poppyseed Muffins
Ingredients and Substitutions
How To Make
How To Store
Air Fry For Magic✨
FAQ: Lemon Poppy Seed Protein Muffins
More Healthy Muffin Recipes
Low Carb Lemon Poppy Seed Protein Muffins
MyFitnessPal Entry
Did You Make This?

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!

Zoomed in view of low carb lemon poppy seed muffins topped with glaze on a plate.

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!

Ingredients and Substitutions

Ingredients for low carb lemon poppy seed muffins.

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!

Ingredients for crumb topping in a bowl before being mixed together.

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

Ingredients for crumb topping in a bowl after being mixed together.

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

Dry ingredients for low carb lemon poppy seed muffins in a mixing bowl before being mixed together.

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.

Wet ingredients for low carb lemon poppy seed muffins in a mixing bowl with a whisk.

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

All ingredients for low carb lemon poppy seed muffins being mixed together in a mixing bowl.

5. Add the dry ingredients to the wet ingredients and fold until combined.

Batter for low carb lemon poppy seed muffins in a muffin tin.

6. Add the batter to the 8 muffin cups.

Crumble topping being added to each  muffin before being baked.

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.

Low carb lemon poppy seed muffins in a muffin pan after being baked.

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.

    How To Store

    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.

    Serious Pro Tip!

    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

    Low carb lemon poppyseed muffins on a cooling rack.

    FAQ: Lemon Poppy Seed Protein Muffins

    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!

    More Healthy Muffin Recipes

    Peanut butter banana oat flour muffins on a tray.

    Peanut Butter Banana Oat Flour Muffins (One-Bowl)

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    Double Chocolate Protein Muffins (100 Calories, 6 Ingredients)

    Banana nut protein muffins with pecan crumble on a tray.

    Banana Nut Protein Muffins with Pecan Crumble

    Honey Whole Wheat Blueberry Greek Yogurt Muffins (one bowl)

    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!

    Lemon poppyseed protein muffins on a plate.
    Rate Recipe Print Pin for Later Share
    4.90 from 19 votes

    Low Carb Lemon Poppy Seed Protein Muffins

    ? Dairy-Free ? Gluten-Free ? High Protein ? Low Carb ? Macro-friendly ? Vegetarian
    These Low Carb Lemon Poppy Seed Protein 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!
    Yield: 8
    Prep: 10 minutes mins
    Cook: 20 minutes mins
    Total: 30 minutes mins
    Calories: 94kcal
    Protein: 8.6g
    Fat: 3.8g
    Carbs: 5.7g

    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

    • Muffin pan

    Notes

    To store: store leftover muffins in an airtight container in the fridge for 4-5 days. Or freeze (in a large baggie with all the air removed) for up to 4 months. Defrost in the fridge overnight or by leaving on the counter for 10-20 minutes.

    Nutrition Information

    Serving: 1muffin (55g), Calories: 94kcal (5%), Carbohydrates: 5.7g (2%), Protein: 8.6g (17%), Fat: 3.8g (6%), Saturated Fat: 2.6g (16%), Fiber: 2.6g (11%), Sugar: 0.7g (1%)

    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.

    MyFitnessPal Entry

    LFF Lemon Poppy Seed Protein Muffins

    © Author: Lauren

    Lemon poppyseed protein muffins on a plate.

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    Lauren

    Lauren lives with her husband, Simon and two dogs, Finley and Cookie, in the Carolina’s. She has college degrees in Nursing and Exercise Science, is a NASM certified trainer and spent many years as a macro coach before transitioning to full time blogging. She loves staying active, being creative and recreating her favorite comfort food dishes into healthier, lightened up versions. Desserts are her speciality!

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    I’m Lauren, a food lover sharing healthy, macro-friendly recipes that taste good and you can feel good about eating. Here you’ll find everything from breakfasts to easy dinners to lightened up desserts because desserts are absolutely mandatory around here!

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