Cinnamon Apple Muffins Recipe

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These cinnamon apple muffins are a delicious sway to revel in the flavors of autumn!

Cinnamon and apples are such a timeless combination, don’t you think? Warm, welcoming and so wonderfully aromatic, you can’t help but get swept away to another time and place.

Clean Eating Cinnamon Apple Muffins Recipe

For me, that time and place is when I was little. It was fall, the weather was cool and damp, pumpkins were everywhere, the school year was still new, and Halloween was just around the corner. Mom had some hot apple cider (with lots of cinnamon) simmering on the stove, and I was busy carving pumpkins. I was definitely in my “happy place”. It felt like total comfort to me.

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Yep, I loved that time of year, and I still do! Maybe it was all that candy, or maybe it was the annual trip to Collinsville, California with my Mom to pick out a pumpkin at the pumpkin patch. But whatever it was, it left a lasting impression with me. And now, every time I make these muffins, I can revisit that time in my memory, and enjoy it almost as much as I did when I was actually carving that pumpkin!


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Clean Eating Cinnamon Apple Muffins

Cinnamon Apple Muffins

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Course: Muffins
Cuisine: American
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 16 muffins
Calories: 134kcal
Author: The Gracious Pantry


  • 2 cups whole wheat pastry flour
  • 2 tsp. baking soda
  • 2 large egg whites
  • ½ cup honey
  • ¼ cup oil (light flavor such as grape seed or safflower)
  • ¾ cup milk (dairy, almond, soy or rice will work well)
  • ½ cup unsweetened apple sauce
  • 1 medium apple (peeled and well chopped)
  • 2 tsp. ground cinnamon


  • Preheat oven to 350 degrees F.
  • In a medium mixing bowl, blend together the flour, cinnamon, chopped apples and baking soda.
  • In a large mixing bowl, whisk together the egg whites, honey, oil, milk, and apple sauce.
  • Pour the flour into the liquid and blend well.
  • Spoon into lined muffin tins and place in the oven.
  • Bake for 15-20 minutes or until the muffins are cooked through (test with a cake tester).
  • Cool on a cooling rack (the apples retain the heat for a while, so allow enough time for cooling).


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


Serving: 1muffin | Calories: 134kcal | Carbohydrates: 23g | Protein: 3g | Fat: 4g | Saturated Fat: 1g | Cholesterol: 1mg | Sodium: 181mg | Potassium: 102mg | Fiber: 2g | Sugar: 11g | Vitamin A: 25IU | Vitamin C: 1mg | Calcium: 26mg | Iron: 1mg
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  1. Hi what is a good substitute for whole wheat pastry flour ..? I can only find whole wheat flour

    1. The Gracious Pantry says:

      White whole wheat flour would be the next best choice.

  2. What substitute to wheat flour would you recommend for your muffins to compensate for gluten intolerance?

    1. The Gracious Pantry says:

      Leah – I’ve never figured that out, I’m sorry. It’s something I’m working on though…

  3. Hello. These look absolutely amazing and I have some apples I need to use NOW! But I was wondering though, is it possible to use coconot flour instead?

    Thank you!

    1. The Gracious Pantry says:

      Angelica – Not for this recipe, no. Sorry…

  4. Can I use oat flour instead?

    1. The Gracious Pantry says:

      Natalie – I don’t recommend it. I have a few gluten free dessert recipes on my blog, but this isn’t one of them. This is formulated to need the gluten.

  5. This recipe is absolutely delicious! It’s not too sweet like many other recipes, it is perfect. Thank you for sharing this!

    1. The Gracious Pantry says:

      Julie – My pleasure! 🙂

  6. Katherine says:

    Made this exquisite recipe, substuting extra applesauce for the oil and adding chopped pecans. It was a hit! I’ll be using this recipe as a base for other delicious breakfast muffins like banana ration, and berry chia. Thanks so much for sharing!

    1. The Gracious Pantry says:

      Katherine – Glad you enjoyed it!

  7. Katherine says:

    This time I substituted pumpkin purée for the applesauce and added nutmeg and pecans. So delicious, thank you again!

    1. The Gracious Pantry says:

      Katherine – My pleasure! Sounds yummy! 🙂

  8. Teresa Tian says:

    Instead of making muffins, is it okay to bake it together in a baking pan/cake pan?

    1. The Gracious Pantry says:

      Teresa – It’s possible, but you’ll have to watch the baking time and I would try to use smaller sized loaf or cake pans. Otherwise, the center may not bake very well.

  9. Teresa Tian says:

    Thank you! I just place the batter into 2 loaf pans and baked it normal temperature and it turned out delicious!

    1. The Gracious Pantry says:

      Teresa – Fantastic!

  10. Is it ok to use wheat flour instead of pastry? Can I sub oatmeal for half the flour? Thank you

    1. The Gracious Pantry says:

      Jessica – Muffins are reliant on the gluten. You can try to sub half the flour, but I can’t guarantee the outcome. As long as the flour is 100% whole grain, it’s clean. But the regular WW flour is a different type of wheat. So you will get a breadier, more dense result.

  11. Made these today as well, love them! Froze half to save for later!

    1. The Gracious Pantry says:

      Monica – You’re on a roll! (pun intended) 😉

  12. Made these this morning they were surprisingly good, will make these again.

    1. The Gracious Pantry says:

      Celeste – Wonderful! My favs are the coconut muffins and the banana muffins. Give them a try if you get a chance!

  13. I tried making your Banana Muffins and they were awesome! Was thinking to add some apples inside. Or rather, add some bananas inside THIS recipe. Will it be okay? Thanks! 😀


    1. The Gracious Pantry says:

      Rusty – Thanks so much! It should be okay, yes. Just don’t overdo it or they won’t bake properly.

  14. I made these this morning! I’m currently living in the UK though and it turns out their idea of applesauce is different than ours so it’s sweet and used for cooking. I used only half the honey and it turned out great only they didn’t rise much. Is that normal?

    1. The Gracious Pantry says:

      Elita – Depends. Are they flat as pancakes or did they raise at least a little bit? There could be a lot of different reasons…

  15. They rose maybe half an inch but that’s about it. They look like cute hockey pucks , but taste amazing.

    1. The Gracious Pantry says:

      Elita – Oh no!! Hmm… Did you forget the baking soda? Or was the baking soda old? Did you use the WW pastry flour?

  16. I did all of the above and bought everything fresh. Maybe I didn’t add enough soda. Anyways they were a big hit regaurdless at our picnic! Thank you!

    1. The Gracious Pantry says:

      Elita – Odd. But I’m glad everyone enjoyed them!

  17. Omg! These are fabulous! My seven year old said they are the best muffins he’s ever tasted. That’s really saying something since his only experience with them is store bought or made from a box.

    Your recipes and advice have been so helpful to me in my quest to go clean. I really appreciate what you do. Thank you!!

    1. The Gracious Pantry says:

      Colleen – That’s wonderful! You made my day! 😀

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