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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
This recipe is absolutely amazing. I did a small batch of 6 as suggested. I added 1 tbsp. chia seeds, 1tbsp. vanilla protein powder and 1 tbsp. vanilla collagen and a few blueberries. It was so good with these healthy additions. I cannot wait for breakfast to enjoy with a cup of strong coffee! Definitely will repeat!
Thank you Maria! So happy you liked them.
I used mayonnaise in place of yogurt because I didn’t have any and they were so good and fluffy! Didn’t affect the taste in my opinion! 10/10 would make again 🙂
Thank you so much for your review! I’m happy you like the muffins 🙂
Worst muffins I’ve ever made they don’t rise at all!
I’m so sorry your muffins didn’t rise, I would check the expiration of your baking powder and soda, it’s possible they are no longer working. Another problem people have had in the past is using a whole wheat flour in place of the whole white wheat flour, these do bake differently. I hope that helps!
Thank you for sharing this recipe. I make these muffins on the regular. My kid loves them and they’re perfect for her school lunch box.
This is a great recipe. I did not do the icing/glaze but I did add some fresh raspberries at the end and gently folded them in.
They were really good. Loved the fresh lemon and they are light and not too sweet. Super easy to make. I doubled the recipe and it worked well. I just had to cook them for an extra two mins (It made 12 total)
I will definitely make these again.
Serving size is unclear. Does this make 12 muffins and the serving size is 2 muffins or does this only make 6 muffins??
This recipe is a small batch recipe and makes 6 muffins.
Love this recipe! I always double it and I add in chia seeds to make it like a lemon poppyseed muffin but healthier!
Love the addition of the chia seeds!