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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 83 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.


  • 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


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


  • 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.




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. 


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!


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.


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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Recipe Rating


  1. Made these today. Super delicious!! We opted not to make the icing, which they were super delish. Thanks for the recipe. 

    1. Hi Noreen! You could use another type of cooking oil, like vegetable oil. Or you can use melted butter also.

  2. These muffins where exactly what I’ve been looking for! Delicious, flavourful and  much healthier than other lemon muffin recipes.I didn’t have enough coconut oil so I used vegetable oil and for the sweetness I added honey! They came up perfect!! 

  3. Yum yum yum! We loved these! We’re pantry baking now so I made some substitutions-agave instead of syrup (I baked at 325) and APF. Moist and delicious!! Only issue was I found the glaze mixture WAY too dry to come together-I added a little more cream and all the juice I had left from my lemon, it was tasty and spread way better. Thanks for this!!

  4. Sooooo….I made these muffins with white flour cuz I didn’t have whole wheat, sour cream cuz I had no yogurt left AND then I FORGOT the egg……..they still were good. A bit of a weird texture cuz of the no egg but still edible. I did not make the icing but it would definately be good!

  5. I’m about to make these cuties, but am so jealous of your muffin pan. Can you share details of it?

    Thanks so much!

  6. I can’t believe how easy and delicious these are!! Almost like cupcakes but way healthier. I did add 2 tablespoons of flaked coconut but it didn’t do much. (Oh well). I used a Neutra bullet blender ingredients. I think it helped with the smooth texture I got. Anyway, they were AMAZING!!

    1. My 4-year old loves these muffins! It is one of the only muffins she will eat, so I make them regularly for lunches and add blueberries or raspberries. The small batch is perfect for the school week. Thank you!

      1. I’m so glad you and your little one enjoy the muffins! Thank you so much for taking the time to leave a review.