Clean Eating Lemon Muffins Recipe

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These delicious clean eating 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 to 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!


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Clean Eating Lemon Muffins Recipe

Clean Eating Lemon Muffins

A delicious snack that travels well!
Print Pin Rate
Course: Dessert, Muffins, Snack
Cuisine: American
Prep Time: 20 minutes
Cook Time: 20 minutes
Total Time: 40 minutes
Servings: 20 muffins (approximate)
Calories: 104kcal
Author: The Gracious Pantry


  • 2 cups whole wheat pastry flour (affiliate link)
  • 2 tsp. baking soda
  • 1 large egg
  • 1/2 cup honey
  • 1/4 cup olive oil
  • 3/4 cup milk (use only 1/2 cup if you are adding frozen fruit like blueberries. Non-dairy milks work too)
  • 2 tsp. lemon extract
  • 1/4 cup lemon zest (freshly grated is best)
  • 1/2 cup unsweetened apple sauce
  • 1/2 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 1/4 cup.
  • Preheat oven to 350 degrees 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. If you put a pan of hot water on the bottom rack while your muffins are baking, they will have the nice high round top that make the store bought muffins look so appealing.

    1. The Gracious Pantry says:

      Adrienne – Thank you! I’ve heard that before but have never tried it. I’ll give it a shot next time. Thanks again!

  2. These muffins look delicious. My favorite muffin flavor… hmm, that’s so hard to say! but right now a banana muffin sounds wonderful.

  3. Mmmm. I was just thinking banana muffins would be good to make today. Thanks again for the link, Tiffany.
    My favorite muffins are bran muffins:
    Preheat oven to 350F
    In a large bowl mix together:
    1 1/2 cups of bran (wheat bran, oat bran or a combo-not bran flakes)
    1 cup whole wheat pastry flour
    1/2 cup raisins
    1/2 cup chopped walnuts
    1 tsp baking powder
    1 tsp baking soda

    In a separate bowl or large measuring cup (2 cups or larger)
    mix together:
    1/4 cup olive oil
    1/2 cup molasses (honey or agave will also work, but change the flavor a lot)
    1 cup milk or unsweetened Silk
    1 egg lightly beaten (or 2 egg whites or EnerG egg substitute)

    Pour the liquid ingredients into the dry and mix lightly, just until everything is moistened.

    Put cupcake papers in muffin tins or spray with olive oil.
    Fill cups about 2/3 full (I use an ice cream scoop!)
    Bake about 20 minutes or until tops spring back when touched lightly or toothpick poked into the center comes out clean.
    These are not excessively sweet. They make a nice breakfast.

    1. The Gracious Pantry says:

      Jodi – Yum! I’ll have to try that! Thanks!

  4. Can never have enough good muffin recipes. I tried this one to day and its a keeper.

    1. The Gracious Pantry says:

      Charlie – That’s great! So glad you enjoyed them!

  5. Anna Johnston says:

    Love a good muffin Tif 🙂 We’re heading off on a road trip tomorrow morning & I’m doing a spot of baking for the trip…, what’s not to like with this recipe. So, thanks 🙂

    1. The Gracious Pantry says:

      Anna – You’re very welcome! Have a great trip!

  6. I love lemon in anything! These sound so yummy

    1. The Gracious Pantry says:

      Aly – Thanks! I bet you’ll love them!

  7. My favorites were pear muffins from a now-defunct coffee shop in Seal Beach. I think I’ll try to create them using your kiwi muffin recipe as a template!

    1. The Gracious Pantry says:

      Molly – That would probably work really well! Let me know how they turn out. I may have to try that too. Sounds yummy!

  8. I just found your website and I am so excited to start exploring. It is just what I am looking for. I just started my clean eating journey so this information is great! Thanks for the time you put into it.

    1. The Gracious Pantry says:

      Heidi – Thanks so much for stopping by! I’m so glad you are enjoying the recipes!

  9. Well, these are the muffins I actually made that day:
    Banana Oatmeal muffins
    Mix in large bowl:
    1 cup Oatmeal (rolled oats)
    1 cup white whole wheat flour
    1 tsp baking powder
    1 tsp baking soda
    In smaller bowl:
    2 bananas mashed with a fork
    1/2 cup unsweetened applesauce
    1/2 cup agave syrup
    1/2 cup milk (or unsweetened Silk)
    1 egg (or 2 egg whites or egg substitute)
    Mix liquid ingredients lightly into dry ingredients.
    Bake in muffin papers about 25 minutes at 350F
    They were YUMMY!

    1. The Gracious Pantry says:

      Jodi – Fantastic! Thank you!

  10. Rose Forever says:

    Those are simple but delicious. My kids love to put some toppings on plain delicious cupcakes. I will try this Clean Eating Lemon Muffins. My favorite muffin flavored is corn flavor. It tastes really sweet and delicious especially with vanilla frosting.

  11. Melanie Giant says:

    This one is great! Lemon for a change coz I am sick of chocolates and pumpkin cupcakes. Lemon and corn are on my mind for some weekend baking activity with my kids. Chocolate syrups are great to add more sweets on the cupcakes. Thanks for the recipe.

    1. The Gracious Pantry says:

      Melanie – If you like corn muffins, I have a great recipe for corn/blueberry muffins here as well. Enjoy!

  12. Delicious! Thank you for this great recipe. I used agave and threw in some frozen raspberries. Yum!

    1. The Gracious Pantry says:

      MK – Y.U.M.!!!

  13. Jamie Glass says:

    Outstanding recipe! I eliminated the oil and substituted applesauce. Cut the lemon out and used frozen blueberries. Wow. These are fantastic and at about 95 calories each, can’t beat it! Good addition to a clean breakfast!

    1. The Gracious Pantry says:

      Jamie – Fantastic! I’m so happy you enjoyed it!

  14. Can I use whole wheat flour or do I have to use pastry flour?

    1. The Gracious Pantry says:

      Amy – Whole wheat flour will work, but the muffins will be a lot more coarse in texture.

  15. I’m back again to say this has become the go-to muffin recipe in my house! I can’t crank them out fast enough, we love them! Thanks so much!!

    1. The Gracious Pantry says:

      MK – Ha! That’s fantastic! I just got a request for my banana muffins at school today. You should try the kiwi muffins too. Delish!

  16. One of my favorite muffins is cranberry-lemon, so I’m going to try this with cranberries!

    1. The Gracious Pantry says:

      Natalie – OooohhMG!!! That sounds so incredible! I might have to try that as well. LOL. It’ll be good stress relief during finals! Great idea!

  17. I have everything I need to make these except lemon zest. Do you think it’d be okay to just add an extra teaspoon of lemon oil? Or any other suggestions?

    p.s. I just started clean eating this week and I LOVE your website, thank you so much for posting these recipes!

    1. The Gracious Pantry says:

      Jen – It will work, but it won’t have the same “true” lemon flavor that the zest provides. I’m sure they would still be good though!

  18. ooh… how about forgetting the blueberries and adding poppy seeds? I LOVE lemon poppy seed bread/muffins….

    1. The Gracious Pantry says:

      Kris – That works too! Enjoy!

  19. Kathy Weber says:

    These are great. I also made them with just regular whole wheat flour. Any ideas where the best place that carries the pastry variety? Whole foods?

    1. The Gracious Pantry says:

      Kathy – Yes, I get mine at Whole Foods in the bulk section.

  20. Tiffany, do you think they’d maintain their taste and bake up OK if I added in some old fashioned oats for heartiness OR a little vanilla whey protein powder for sticking power? Just thinking about some fun tinkering…thanks and LOVE your blog! My new go-to for recipes.

    1. The Gracious Pantry says:

      Michelle – Thanks! I’m happy you’re enjoying my recipes! Yes, you can put oats or whey in, but you will have to reduce the flour, otherwise they will be too dry. Let me know how they turn out!

  21. 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!

  22. 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.

  23. 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!

  24. Anonymous says:

    Jamie – Great! Glad you found something you like!

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

    1. Anonymous says:

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

  26. Anonymous says:

    Amber – What a great idea! Enjoy!

  27. 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!

  28. graciouspantry says:

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

  29. 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.

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

    1. The Gracious Pantry says:

      Kellen – My pleasure!

  31. 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.

  32. Mmmmm… A DELICIOUS take on healthy muffins. 🙂 I subbed coconut oil and it turned out fantastic! Thanks!

    1. The Gracious Pantry says:

      Melanie – My pleasure!!

  33. 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.

  34. 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 🙂

    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. 🙂

  35. I made these today, is there a way to make them more lemony in flavor? I like them, I just want more lemon! 🙂 Can I double the extract?

    1. The Gracious Pantry says:

      Monica – Sure! And lemon zest will help too!

  36. 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.

  37. 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! 😀

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