Cinnamon Apple Muffins Recipe

Prep Time 15 mins
Total Time 35 mins
Servings 14 muffins

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These Cinnamon Apple Muffins are so moist and loaded with apple chunks, unsweetened applesauce and cinnamon. They are big on flavor and made with healthier ingredients.

cinnamon apple muffins on a plate on grey background with halved apples in the background
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Table of Contents
  1. How to make Cinnamon Apple Muffins:
  2. What makes these Apple Muffins healthy?
  3. How to freeze apple muffins:
  4. Can I make these apple muffins into apple bread?
  5. Cinnamon Apple Muffins Recipe

Muffins, breads, baked goods — they are always a hit around here. These Apple Muffins are no exception!

I know you are probably over apples already and I should be on to peppermint and Christmas baking, but I’m not letting go. Fall is just getting started, and I’m going to hang onto this beautiful season as tight as I can before we’re hit with the first big snow!

With our oldest in grade 1 this year and my husband still busy and gone 14 hours per day, we’re packing a lot of lunches (and those of us who aren’t packing lunches still need snacks! Just ask my 3 year old 😉 ).

I love to have a big stash of muffins and quick breads in the freezer for quick breakfasts (you know, just in case my kids ever sleep past 6:30 am…..) and something hearty to stick in lunch boxes.

There’s not guarantee that the veggies in my 6 year old’s lunch box will get eaten, but breads and baking? Pretty much a given! For this reason, I like to load my baking up with the healthiest ingredients I can without sacrificing flavor.

How to make Cinnamon Apple Muffins:

  • Choose the right apples. Generally, firmer apples work better for baking because they don’t turn to mush in the oven. You also want a sweet-tart flavor that will really pack a punch in any baked goods. See this article for choosing good baking apples.
  • Don’t overmix. Mixing the muffin batter too much can give you tough, dry muffins, so go easy and mix just until all the dry goods are incorporated.
  • Don’t overbake. This is pretty much my favorite baking tidbit for any baked good, because I love my baking to be moist or chewy or luscious but definitely not dry and overbaked. You want to bake until the centers are completely set, but not much past that point or you will have dry lumps of muffins.
cinnamon apple muffins up close on white plate with whole apples in the background

What makes these Apple Muffins healthy?

For this recipe, I used whole wheat flour, unsweetened applesauce and Greek yogurt instead of butter, and rely mostly on the natural sweetness of the apples (although there is still some sugar!). This makes these muffins a healthier but still delicious lunch or breakfast option!

How to freeze apple muffins:

These Apple Muffins freeze perfectly in an air tight container or freezer bag. You can store them up to 3 months.

To thaw, you can leave out on a plate for an hour or two at room temperature, or microwave on low heat for roughly 1-2 minutes.

Can I make these apple muffins into apple bread?

Absolutely! This muffin recipe is adapted from this Praline-Glazed Apple Bread, so check over there for detailed recipe instructions 🙂

cinnamon apple muffins on a plate with a bite taken out of one muffin

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Cinnamon Apple Muffins

5 from 1 vote
These Cinnamon Apple Muffins are so moist and loaded with apple chunks, unsweetened applesauce and cinnamon. They are big on flavor and made with healthier ingredients.
Prep Time 15 mins
Cook Time 20 mins
Total Time 35 mins
Cuisine American
Course Bread and Baked Goods
Servings 14 muffins
Calories 194cal


  • 1 cup 0% plain Greek yogurt (250g)
  • ½ cup unsweetened applesauce (115g)
  • 2 large eggs
  • ¼ cup milk or buttermilk
  • 2 teaspoons vanilla
  • 1 cup brown sugar* lightly packed (210g)
  • 2 teaspoons baking powder
  • 1 teaspoon baking soda
  • 1 teaspoon cinnamon
  • ½ teaspoon salt
  • cups whole wheat flour fluffed (325 grams)
  • 2 Granny Smith or baking apples peeled and finely chopped (3 cups or 315 grams apples)

Cinnamon Sugar (optional)

  • 2 tablespoons melted butter
  • 3 tablespoons sugar
  • 1 teaspoon cinnamon


  • Preheat oven to 350 degrees F.
  • In a large bowl, whisk together yogurt, applesauce, eggs, milk, vanilla and brown sugar until smooth. 
  • Add baking powder, baking soda, cinnamon and salt and whisk until combined.
  • Fold in flour and apples with a spatula, just until moistened and no flour remains. 
  • Lightly grease a non-stick muffin pan or fill with paper liners, and fill muffin cups to the top (you can also make smaller muffins but they will bake more quickly).
  • Bake for 20-25 minutes, until a toothpick inserted in the center comes out clean or with moist crumbs. Let cool for 5-10 minutes in the pan before removing to a wire rack to cool completely. (If using paper liners, they will be easier to remove after several hours has passed)

Cinnamon Sugar (optional)**

  • Brush butter over tops of slightly cooled muffins.
  • Stir together cinnamon and sugar. Sprinkle over muffins before serving.
  • Store muffins uncovered at room temperature on the day you bake them. To store longer, place in an airtight container and refrigerate up to 5 days or freeze up to 3 months.


*These muffins are not overly sweet but I find them perfect with the cinnamon sugar topping. If you are not going to use the topping, or you like muffins a little sweeter, you can add an extra ¼ cup sugar to compensate.
**Muffins with the cinnamon sugar topping are best eaten that day. Once they are sealed and stored, the sugar will lose its crispness and become moist. They are still tasty, it is just the texture that will change. 

Nutrition Information

Calories: 194cal | Carbohydrates: 38g | Protein: 5g | Fat: 3g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 1g | Cholesterol: 29mg | Sodium: 197mg | Potassium: 228mg | Fiber: 3g | Sugar: 21g | Vitamin A: 111IU | Vitamin C: 1mg | Calcium: 75mg | Iron: 1mg
Keywords apple bread, apple cinnamon muffins, apple muffins, healthy apple muffins

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Meet Ashley

My name is Ashley Fehr and I love creating easy meals my family loves. I also like to do things my way, which means improvising and breaking the rules when necessary. Here you will find creative twists on old favorites and some of my favorite family recipes, passed down from generations!

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Reader Interactions


  1. Luke says

    I used 2 smaller Granny Smith apples, which was 270 grams. This was definitely too much apple. I would recommend perhaps in the 200 – 225 gram range for the apples. Even less if adding nuts or raisins, although I didn’t try that.
    Also, these will stick to paper liners, so you may want to spray the liners.
    Overall the recipe is good. Moist and not too sweet.
    Note: I made the recipe exactly as written.

    • Ashley Fehr says

      Thanks Luke! Did you try removing the muffins from the liners the next day? I find that with most muffins they need to sit overnight at room temperature before they’ll remove easily from the liners.

      • Luke says

        I did have a slightly easier time removing the muffins from the liner the next day. But, what really helped was switching to parchment liners! They are absolutely a game changer when cooking healthier (particularly lower fat) muffins. I got the ones that look like classic cupcake/muffin liners, not the “bakery” style.

  2. Maureen Brezynskie says

    I made these muffins this morning and they are delicious. One of the easiest and best apple muffin recipe I have made. I added walnuts and they are so moist and tasty. I love your recipes! Thanks!

  3. Patricia says

    My daughter is celiac and all “healthy “ baked goods calls for whole wheat flour. Any idea for substitute.

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