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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
Yummy recipe!
Made these today. Super delicious!! We opted not to make the icing, which they were super delish. Thanks for the recipe.
Hi, what could I replace with coconut oil? thanks
Hi Noreen! You could use another type of cooking oil, like vegetable oil. Or you can use melted butter also.
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!!
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!!
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!
I’m about to make these cuties, but am so jealous of your muffin pan. Can you share details of it?
Thanks so much!
Oh wait! I didn’t look hard enough and see it now.
oops. 🙂
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!!
Can i use AP flour?
Any changes to a baking recipe, including a different flour will change the outcome.
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!
I’m so glad you and your little one enjoy the muffins! Thank you so much for taking the time to leave a review.
This recipe was great! I will for sure be making this again! Thank you so much!!