Lemon Muffins Recipe

These delicious lemon muffins make a perfect, take-along snack!

A Facebook fan recently asked me if I could come up with a recipe for Lemon Blueberry Muffins.

Since I already had a Blueberry Corn Muffin recipe, I figured I would try a lemon muffin and really focus on the lemon flavor. The thing is, when you bake with whole grains, flavors like lemon can be difficult to really bring to the forefront (at least for me). So this was a major point of focus for me.

Clean Eating Lemon Muffins Recipe

If you like the idea of adding blueberries, feel free to do so. It would certainly be tasty!

More Healthy Muffin Recipes

Lemon Muffins Recipe Card

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Clean Eating Lemon Muffins Recipe

Lemon Muffins

A delicious snack that travels well!
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Course: Dessert, Snack
Cuisine: American
Prep Time: 20 minutes
Cook Time: 20 minutes
Total Time: 40 minutes
Servings: 20 muffins (approximate)
Calories: 104kcal


  • 1 Standard muffin pan


  • 2 cups whole wheat pastry flour (affiliate link)
  • 2 tsp. baking soda
  • 1 large egg
  • ½ cup honey
  • ¼ cup olive oil
  • ¾ cup milk (use only ½ cup if you are adding frozen fruit like blueberries. Non-dairy milks worsk too)
  • 2 tsp. lemon extract
  • ¼ cup lemon zest (freshly grated is best)
  • ½ cup unsweetened apple sauce
  • ½ cup blueberries (optional)


  • If you use fresh fruit, don't make any adjustments. Just add the fruit. However, if you are using frozen fruit, reduce the milk by ¼ cup.
  • Preheat oven to 350° F.
  • Line your muffin tin with cupcake papers or spray the tin with an olive oil mister.
  • In a medium mixing bowl, whisk together your flour and baking soda.
  • In a large mixing bowl, blend the rest of the ingredients using a whisk.
  • Add the flour to the wet ingredients a little at a time, whisking as you go.
  • Pour into your muffin tin. Fill up the cups only half way.
  • Bake for 20 minutes or until a toothpick poked in the middle of a muffin comes out clean.


Please note that the nutrition data below is a ballpark figure. Exact data is not possible.


Serving: 1muffin | Calories: 104kcal | Carbohydrates: 17g | Protein: 2g | Fat: 3g | Cholesterol: 10mg | Sodium: 143mg | Potassium: 72mg | Fiber: 1g | Sugar: 8g | Vitamin A: 30IU | Vitamin C: 2mg | Calcium: 18mg | Iron: 0.6mg

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  1. These were fantastic! My family sometimes teases my clean eating attempts but the entire batch disappeared before lunchtime. Thanks. : )

    1. The Gracious Pantry says:

      Rachel – That’s wonderful!! And when you’re the one that is healthy, you’ll be the one with the last laugh. Hang tough girlfriend!

  2. Don’t have lemon extract, can I use lemon juice?

    1. The Gracious Pantry says:

      Amy – You can try it, but I don’t think it will be the same. Try more lemon zest instead.

  3. Are you really supposed to use 4 tablespoons of zest? It seems like that would be too much. I was wondering if it’s supposed to be 4 teaspoons.

    1. Anonymous says:

      Becky – No, tablespoons is right!

  4. Anonymous says:

    Jamie – Great! Glad you found something you like!

  5. Absolutely wonderful muffins! Thank you for the recipe!

    1. Anonymous says:

      Sherri – Fantastic! I’m glad you enjoyed them!

  6. Anonymous says:

    Amber – What a great idea! Enjoy!

  7. onevoice84 says:

    These were great!! The only modification I made is I like to add flax seed to muffins 1/2 cup in place of 1/2 cup of flour, makes it even healthier. If you do this I would increase the lemon zest by a tablespoon but they turned out wonderful! I used frozen all natural blueberries a little under a cup and next time I would probably put a full cup in (no such thing as too many blueberries!) Thank you so much for this recipe, I always eat muffins as my mid morning snack because they are so easy to freeze and make in mass. This recipe was simple and easy. Definitely will make them again!

    1. graciouspantry says:

      onevoice – Glad you enjoyed them!

  8. graciouspantry says:

    onevoice – Thank you so much! You made my day!

  9. This is a general question for all recipes, not just this one: Can coconut oil be used in place of olive/sunflower/safflower oil?

    1. The Gracious Pantry says:

      Jen – Yes it can.

  10. Just starting the clean eating transition….this is a great recipe! Thank You!

    1. The Gracious Pantry says:

      Kellen – My pleasure!

  11. If I wanted to make this in bread form (large loaf pan), what are your recommended alterations to the cook time, etc.?


    1. The Gracious Pantry says:

      Kaitlin – I’m not sure as I haven’t tried. But definitely keep the loaf small and then check it about every 2-3 minutes after the cooking time called for in the recipe.

  12. Mmmmm… A DELICIOUS take on healthy muffins. ๐Ÿ™‚ I subbed coconut oil and it turned out fantastic! Thanks!

    1. The Gracious Pantry says:

      Melanie – My pleasure!!

  13. Can I substitute coconut flour for the wheat pastry flour?

    1. The Gracious Pantry says:

      Hannah – I’m afraid not. Coconut flour is a very different animal than wheat flour.

  14. I made these last night! I had to substitute regular whole wheat flour instead of pastry and fresh lemon juice instead of extract since I didn’t have either but they turned out great! I love that the sweetness is very subtle. Most muffins seem too dessert-like these days, but this was the perfect breakfast muffin ๐Ÿ™‚

    1. The Gracious Pantry says:

      Britni – I’m so glad they turned out! It’s always been my philosophy that a huge amount of sweetness should be reserved for cupcakes. Not muffins. ๐Ÿ™‚

  15. I made these today, is there a way to make them more lemony in flavor? I like them, I just want more lemon! ๐Ÿ™‚ Can I double the extract?

    1. The Gracious Pantry says:

      Monica – Sure! And lemon zest will help too!

  16. Help! I just made these this morning. Love the flavor, but the middle turned out gummy. I’m trying to figure out why so I don’t make the same mistake again next time. I only made two minor changes: I replaced half of the oil with applesauce and I didn’t have lemon zest so I just added another teaspoon of lemon extract. Other than that, I followed the recipe. Although, now that I think about it, my baking soda might be a little old. Not sure if that could be the cause. After the first batch cooled a little, I tried removing one from the wrapper and I noticed the gummy-ness. I thought maybe they weren’t baked enough, so I put them back in for another 10 minutes. That helped some, but the texture is still a little gummy. I’d be afraid to bake them for much longer as they were pretty dark after 30 minutes. Any idea what I did wrong?

    1. The Gracious Pantry says:

      Tami – It’s probably due to using apple sauce instead of oil as that would add more moisture (just a guess). But if you feel that baking them longer would help, just put a piece of aluminum foil loosely over the top of the muffins once they are nearly brown. It will keep the tops from burning. Also, be sure your oven is baking at the temp that is say it is. Some ovens vary greatly from the temperature on the dial. A simple oven thermometer will tell you. Any kitchen supply place will have them and they run about $8. Definitely a worthwhile investment.

  17. I made these tonight and had to use orange zest because I ran out of lemons. I also used half and half raw honey and maple syrup. These muffins were so moist and delicious and a hit with everyone!

    1. The Gracious Pantry says:

      Jennifer – Fantastic!! I’m so happy everyone loved them! ๐Ÿ˜€