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These healthier lemon muffins are bright, fluffy, and naturally sweetened with maple syrup—perfect for a quick breakfast or snack. Made in one bowl with simple ingredients, they’re easy to whip up and bursting with fresh lemon flavor!
Looking for more baking recipes for breakfast? Try our Banana Bread Crumb Cake, Easy Cheese and Sausage Biscuits, or Buttermilk Waffles next!
Fresh, Lemony, and Just Sweet Enough
Lemon muffins, but make them better. You know I love a good bakery-style muffin—the kind that’s fluffy, sweet, and absolutely loaded with bright lemon flavor—but sometimes I want one that feels a little more balanced.
Enter these healthier lemon muffins: soft, citrusy, and just the right amount of sweet, made with fresh lemon juice, white whole wheat flour, coconut oil, Greek yogurt, and maple syrup. They’re the kind of muffin that makes your kitchen smell incredible and somehow feels like a little burst of sunshine in snack form.
Perfect for busy mornings, afternoon pick-me-ups, or whenever you just need something lemony and delicious.
Why You will Love This recipe
- One bowl & simple ingredients – Easy prep with common pantry staples!
- Small batch – Just enough for breakfast, but easy to double.
- Naturally sweetened – Maple syrup + whole wheat flour for a wholesome treat.
Ingredients You Need
- Flour – Use white whole wheat flour for a wholesome touch or all-purpose flour for a classic texture. A 50/50 mix works too! Keep in mind that white whole wheat flour is different than regular whole wheat.
- Coconut oil – Keeps the muffins moist. Swap with melted butter or a neutral oil (like avocado or vegetable) if preferred.
- Greek yogurt – Adds moisture and a slight tang. Substitute with sour cream or plain yogurt. You could even blend up some cottage cheese to use in this recipe.
- Egg – Helps bind everything together. Use a flax egg (1 tbsp flaxseed meal + 2.5 tbsp water) for an egg-free option.
- Maple syrup – Naturally sweetens the muffins.
- Honey works too, but will slightly alter the flavor.
- Fresh lemon juice & zest – The star of the show! Fresh is best, but bottled lemon juice can work in a pinch (though you’ll miss the zest).
- Baking powder & baking soda – Gives the muffins a fluffy rise. Make sure they’re fresh for the best results!
- Salt – Enhances flavor—don’t skip it!
- Vanilla extract – Adds warmth and balances the lemony brightness.
Optional Glaze
These muffins are perfectly delicious on their own, but if you want to take the lemon flavor up a notch, a simple glaze is a fun addition! It adds a sweet, tangy finish and makes the muffins feel a little extra special. Want to keep things lighter? Skip it—these muffins are just as good without!
How to make Healthier Lemon Muffins
Find the complete recipe card below with measurements and full instructions.
- 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 Information
- Room Temperature: Store muffins in an airtight container for up to 2 days.
- Refrigerate: For longer freshness, keep them in the fridge for up to 1 week—just warm them slightly before eating!
- Freeze: Let muffins cool completely, then freeze in a sealed bag for up to 3 months. Thaw at room temp or microwave for a quick refresh.
- Glaze separately: If using a glaze, store it separately and drizzle just before serving to prevent sogginess.
Recipe Tips
- Zesting first – Zest lemons before juicing for easier prep and less waste.
- Extra lemony? Add a splash of lemon extract for more punch.
- Thick batter is normal – It’s fluffy, not smooth! Bakes up moist and tender.
- Glaze last minute – Store muffins unglazed to avoid sogginess. Skip the glaze if you prefer less sugar!
More Baking Recipes
Healthier Lemon Muffins (Small Batch)
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
- ⅓ 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
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
More Baking Recipes
Recipe first published April 1, 2016. Updated May 28, 2020, and February 3, 2025.
Photography by KJandCompany.co
Just finished making these they are so light and fluffy. In keeping them healthier tho I am not adding the icing and I don’t think it needs it. Very delicious
These muffins are delicious and will be !
These muffins are wonderful.
Very good and fluffy! Followed recipe,but used regular peach yogurt since didn’t have Greek one and it turned out still delicious.
Have you tried this with almond or coconut flour? Is there a way to make them fluffy while using a mixture of these flours?
Sorry, I haven’t tried this so I’m not able to verify if it will work.
This is by far the best muffins I have ever made. I’m 15 and I’m new to baking and cooking. I made this today and my family and I loved the muffins, especially with the glaze. It was really delicious. Thank you so much 😸
Delicious! I added flaked almonds with raspberries, they were so good 🙂 going to make another batch!
They are delicious! Thanks for sharing! Do you think I could make them in to a cake?
I’m so glad you enjoyed the recipe. Since I haven’t tried to bake this into a cake, I can’t speak on if it will work or not. If you try it out please let me know.
This is one of the best muffins I have ever eaten. Absolutely delicious! I followed the directions exactly except I used vanilla flavored Greek yogurt, and like some one else mentioned, also found the glaze to be too dry. Just a little bit more milk and lemon juice did the trick. Thank you for an amazing recipe.
Will make again soon. They were light and fluffy and had a light lemon flavour that my husband loves but I may add a tad more to it. So yummy that I would double it next time, thank you for a great lemon muffin!