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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
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. 🙁
So, you completely changed the recipe and it didn’t turn out?
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!
1 cup mean how much in gm?
Would I need to alter the recipe if I used fresh ground whole wheat flour? Maybe a little more yogurt or possibly some buttermilk?
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.
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!
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!
Did mini muffins w/ a small scoop of chia seeds. The teenager loved them
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.
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.
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!
I mean to say I didn’t know what “white whole wheat” is.
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.
I’m so glad the you and your little one loved the muffins! Thanks so much for taking the time to comment! xo
wonder what the nutrition facts for these muffins
Those muffins look killer! I can’t wait to make them and scruff em down for movie night tonight!
Thanks so much! I hope you enjoyed 🙂