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Healthy Lemon Muffins. This small batch of healthier lemon muffins will definitely brighten up your breakfast in the morning. Made with coconut oil, greek yogurt, and fresh squeezed lemon juice. 

Lemon muffin sitting in a white cupcake liner, with a light white drizzle on top. Bowl of icing with a spoon behind the muffin.


 

Healthier lemon muffins. Start the day off right with these EASY to make, skinny lemon muffins.

  • Simple to make: only one bowl and common pantry items are needed for this recipe! 
  • Small batch: the perfect amount for me and my kids for breakfast with no leftovers. But it’s so easy to make a larger batch if needed.

How to make Healthier Lemon Muffins:

  1. Wet ingredients: combine the wet ingredients. Be sure that the coconut oil is melted but not hot when mixing. Allow time for it to cool to room temperature before mixing.
  2. Dry ingredients: add the dry ingredients to the mixed wet ingredients and stir until just combined. 
  3. Scoop: add the muffin batter to the muffin tin. 
  4. Bake: be sure to check the muffins with a toothpick to ensure they are baked through.
Picture collage showing how to make healthy lemon muffins, showing wet ingredients in a bowl, mixed together. Adding dry ingredients. Then the mixed batter.

Ingredient Breakdown:

  • White Whole Wheat Flour: this is different than whole wheat flour since it’s harvested from different wheat. Whole wheat flour is ground red wheat which gives the color and texture that you know as whole wheat flour. White whole wheat flour is ground white wheat, it is NOT bleached. It’s a light flour that bakes similar to all purpose flour. And it does have the same nutrients as using regular whole wheat flour. 
  • Coconut Oil: adds moisture and gives a wonderful hint of coconut flavor to the muffins.
  • Maple Syrup: to sweeten. Can also be subbed with honey. 
  • Greek Yogurt: extra moisture. Plus if you use a vanilla or lemon flavored yogurt it will give an extra boost of flavor.
  • Baking powder and baking soda: due to the amount of acidic ingredients both are used to give the right amount of lift. 
  • Lemon: fresh squeezed lemon juice and zest give a bright flavor to the muffin.
  • Egg
  • Salt
  • Vanilla extract

Pro Tips:

  • Zesting: Zest the lemons first then juice them. This makes it easier to get the zest and leads to less waste of the lemons. 
  • More Lemon Flavor: feel free to add a bit of lemon extract on top of the fresh lemon juice if you’re wanting extra lemon flavor in your muffins.
  • Texture: the batter for these muffins might look thick, it’s a fluffy batter, not a smooth creamy batter. So don’t worry! These muffins will bake up moist and tender. 
  • Glaze right before serving: don’t store glazed muffins as the glaze can become soggy. Store the glaze separate and drizzle right before serving. But keep in mind the glaze is NOT necessary. If you’re wanting to cut the sugar completely skip it. 
Lemon muffin in a white paper, with a bite missing showing the texture of the baked muffin.

More Muffin Recipes:

Healthier Lemon Muffins (Small Batch)

4.99 from 81 votes
Prep: 5 minutes
Cook: 16 minutes
Servings: 6
Author: Serene
This small batch of healthier lemon muffins will definitely brighten up your breakfast in the morning. Made with coconut oil, greek yogurt, and fresh squeezed lemon juice.
Lemon muffin sitting in a white cupcake liner, with a light white drizzle on top. Bowl of icing with a spoon behind the muffin.

Ingredients  

  • 1 cup white whole wheat flour or all purpose flour
  • ½ tsp baking soda
  • ½ tsp baking powder
  • 1/4 tsp salt
  • ¼ cup coconut oil melted
  • ¼ cup maple syrup
  • 1 large egg
  • cup plain greek yogurt
  • 1 tsp vanilla extract
  • 2 tbsp lemon juice freshly squeezed
  • Zest from 1 lemon

Icing

  • ½ cup powdered sugar
  • ½ tsp almond milk/milk/cream
  • ½ tsp lemon juice freshly squeezed
  • ½ tsp vanilla extract

Instructions 

  • Preheat oven to 350°F. Spray muffin tin with baking spray or line with paper liners and set aside.
  • In a medium size mixing bowl add the melted and cooled coconut oil, maple syrup, egg, greek yogurt, lemon juice and vanilla extract. Stir to combine.
  • Add the flour, baking soda, baking powder, salt, and lemon zest to the mixing bowl. Stir just until combined.
  • Spoon the batter into the muffin tin to 3/4 full, there will be enough batter for 6 muffins.
  • Bake for 16 minutes or until tops are puffy and a toothpick inserted into the center comes out clean.
  • Remove from the oven and allow to cool for about 5 minutes then remove from the muffin tin to a wire rack to continue cooling.
  • To make the icing combine all the ingredients in a small bowl and stir to combine. Drizzle over the muffins.

Video

Equipment

Notes

Storage: store in a sealed container at room temperature without any glaze. Muffins can be stored for up to 3 days. 
Freezing: wrap individually and then store in a sealed freezer safe container. Thaw at room temperature before serving. 

Nutrition

Calories: 208kcal | Carbohydrates: 36g | Protein: 4g | Fat: 6g | Saturated Fat: 4g | Cholesterol: 28mg | Sodium: 257mg | Potassium: 51mg | Fiber: 2g | Sugar: 22g | Vitamin A: 40IU | Vitamin C: 1mg | Calcium: 49mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Like this? Leave a comment below!

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Recipe first published April 1, 2016. Updated May 28, 2020 with new images and changes to recipe of more coconut oil and yogurt for added moisture.

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Welcome to my kitchen!

Welcome to the House of Yumm!! My name is Serene. I’m the food photographer, recipe developer, and official taste tester around these parts.

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45 Comments

  1. I hate to leave a bad review, but the recipe does not have enough liquid ingredients in proportion to the dry ingredients so I doubled the liquid ingredients. The muffins took twice as long to cook and when I pulled them out of the oven, they collapsed on themselves. 🙁

      1. Hello!
        I also did not have enough liquid, but I’d subbed a dry sweetener since I did not have agave (though it still was dryer than muffin recipes I was used to?). I ended up adding about 2 tablespoons of almond milk and they turned out perfect and fluffy. Thanks!

  2. Would I need to alter the recipe if I used fresh ground whole wheat flour? Maybe a little more yogurt or possibly some buttermilk?

    1. Hi Kris! Yes, the recipe would need to be altered. Typically whole wheat flour changes the texture of baked goods. Which is why I love using the white whole wheat because it bakes like an all purpose flour. If you want to substitute out some of the white whole wheat with ground whole wheat you could swap in 25% without noticing much difference in the texture. But if you use all fresh ground whole wheat flour the muffin recipe will turn out quite different. It’s something that would need to be experimented with to get it the way you want.

  3. these tasted so good! my mom will only eat healthy stuff and any muffin recipe i came across had 1 cup sugar and/or 1 cup of butter. then i found this recipe. absolutely divine!

  4. I was a bit worried how they would turn out, because the batter was rather thick, however…. they turned out awesome!!!! Even my 2 boys liked them! Next time I will try and add some more lemon/zest or lemon EOs to make them more lemony… but they were fabulous!

  5. Hi there! I followed your recipe to a t and they dough ended up being super dry. I had to add some more yogurt to try to save it but the end result looks like little balls of dried up dough. Booo! I used coconut oil, and honey. The consistency of the dough was just super rough. Any ideas what happened? I used whole wheat flour too.

    1. The recipe calls for White Whole Wheat flour, which bakes similar to all purpose flour. Swaping that with a regular whole wheat flour would change the texture of the muffin.

  6. I was skeptical this wouldn’t be lousy, but let me freely admit I am OBSESSED with this recipe after tasting it. I made it with whole wheat flour, since I don’t even know what “whole whole wheat” is, and i used maple syrup, coconut oil and lemons right off the tree, Strangely, I have a hard time picking up much of the lemon flavor, but the gentle blend of coconut, wheat & lemon-whiff flavors are perfectly balanced. I’m especially a fan of the texture and lack of “egginess” that can taint a low-cal muffin. Kudos!

  7. Made these cuties today. I must say it’s moist, extremely soft & fluffy. It definitely is healthy and my little Toddler simple loved it. I scooped the batter in the mini cupcake pan and baked it for 10 min, it was perfectly baked. I used multigrain wheat flour, probably why my cupcakes didn’t look crisper at the top. I think I love it the way it turned out. Thank you for this simple Recipe.

  8. Those muffins look killer! I can’t wait to make them and scruff em down for movie night tonight!