One of our favorite fall flavors is apple, and what better way to enjoy apples than in these homemade Healthy Apple Cinnamon Muffins?! Topped with a streusel topping and cream cheese frosting drizzle…oh my! While this post is sponsored by our friends at Crispy Green, the recipe and our love for these apple muffins are our own.

Best Healthy Apple Cinnamon Muffins

I love fall, the weather starts to cool down and we are surrounded by comforting scents, eats, treats and memories. One of my favorite fall flavors is apple, I have the best memories of visiting apple orchards when I was a kid back in Michigan and of taking my kids. There’s just something about grabbing that cup of hot apple cider and a warm cinnamon-sugar covered donut that completed all things fall for me when I was a kid. Now that I live in Florida, I still crave the fall flavors that bring back those heart-warming memories.

Easy Healthy Apple Cinnamon Muffins

That’s just one reason why I love these apple cinnamon muffins. Oh the way your kitchen smells while these are baking is just divine! I mean, Hello Fall! Added bonus that I actually found a way to make these delicious muffins lower in fat than the ones you typically see cruising around the internet and on Pinterest. We are all about healthy recipes that the whole family will love here at Healthy Family Project 🙂

Tasty Healthy Apple Cinnamon Muffins

Here’s a fun fact…Did you know that the United States grows approximately 200 unique apple varieties? That’s a lot of different apples! And I would bet that each one is delicious in it’s own way.

From Granny Smith to Honeycrisp, there’s an apple for everyone. And with new varieties being created all the time, there’s always something new to try.

Maybe it’s the sweet taste, or the juicy texture. Whatever the reason, apples are one of the most popular fruits out there.

Healthy Apple Cinnamon Muffins

Not only are apples delicious, but they’re also good for you. We all know the saying….An apple a day….

Healthy Apple Cinnamon Crumble Muffins

Why We Love Apples, Especially In The Fall

When it comes to fall flavors, apples are at the top of the list. Here are a few reasons why apples are one of our favorite fall flavors:

1. Apples are in season during fall. This means that they’re fresh and at their peak flavor.

2. Apples go great with other fall flavors like cinnamon and pumpkin spice.

3. Apples are versatile fruits that can be used in sweet or savory dishes, like these Chicken and Apple Enchiladas.

4. Apples can be eaten fresh, cooked, or baked. This makes them a great option for all your favorite fall recipes and beyond.

Healthy Apple Cinnamon Struesel Muffins

Which Apple is Best for Baking?

When you are using apples in baking, like with our yummy healthy apple cinnamon muffins, there are a few things to consider when picking the apple. One thing to consider is moisture; moisture is key to ensuring your baked goods are soft and fluffy. The second is sweetness; you want your baked goods to be sweet, but not too sweet.

So, which apple is best for baking?

Granny Smith apples are used quite a bit in baking. They’re tart and acidic, which helps to balance out the sweetness of the other ingredients in your recipe. They also have a firm texture that holds up well in the oven.

Honeycrisp apples sweeter, which makes them great for eating, not always in baking.

My husband currently has an envy apple addiction, so I had two bags on my counter, so that’s what I used in my muffins and they were excellent.

I recommend using a firmer apple when baking so that it holds up. If your apple is on the sweeter side, that may be okay for this apple muffin recipe since I didn’t use much sugar, the sweetness comes from the apples and Crispy Green Freeze-Dried Apples.

Apple Cinnamon Muffins

Cinnamon Apple Muffins Key Ingredients

I know the ingredient list is a little longer than what we typically share, but these muffins are made from scratch and have three different parts. If you don’t want to make the crumb topping, feel free to leave it off…not a fan of cream cheese frosting, you don’t have to make it! A lot of these key ingredients are pantry staples, the only thing I had to grab at the store was the unsweetened applesauce.

I used freeze-dried apples in the muffin mix, as part of the crumble topping and in the cream cheese icing. Using the freeze-dried apples added a natural sweetness and heighten the apple flavor.

How to make Healthy Apple Cinnamon Muffins

Storing Homemade Apple Cinnamon Muffins

You can store your homemade apple muffins in an airtight container on the counter for a few days or in the refrigerator for about a week. My guess is that they won’t last that long though 😉 You can also freeze these healthy apple muffins! I recommend wrapping them individually in press n’ seal or freezer wrap then putting them in a freezer-safe container or freezer bag. Make sure they have cooled down before freezing. Your muffins will keep in the freezer for about 2 months.

Apple Cinnamon Muffins with Crumble Topping


Q: How long do you bake healthy apple cinnamon muffins?
A: Bake at 425F for 5 minutes, then reduce heat to 350F and bake 15 more minutes.

Q: What do you need to make healthy apple cinnamon muffins?
A: Ingredients include flour, baking soda, cinnamon, eggs, yogurt, applesauce, vanilla, brown sugar, olive oil, apples.

Q: What makes these apple cinnamon muffins healthy?
A: They are made with Greek yogurt and applesauce instead of oil or butter for a lower fat muffin.

Q: How do you make the crumb topping for apple cinnamon muffins?
A: Mix together butter, flour, brown sugar and cinnamon.

Q: What kind of apples work best for apple cinnamon muffins?
A: Firmer apples like Granny Smith or Envy hold up well during baking.

Q: How do you store leftover apple cinnamon muffins?
A: Store in airtight container at room temperature up to 1 week, or freeze up to 2 months.

Q: What do you drizzle on apple cinnamon muffins?
A: Make a cream cheese frosting with cream cheese, butter, milk, sugar and freeze dried apples.

Q: How many muffins does this apple cinnamon recipe make?
A: This recipe makes approximately 15 muffins.

Q: Are these apple cinnamon muffins vegetarian?
A: Yes, they are vegetarian.

Alright, let’s get baking!

Healthy Apple Cinnamon Muffins

Healthy Apple Cinnamon Muffins with Streusel Topping

Tracy Shaw
The house will smell absolutely amazing while you bake up a batch (or two!) of these apple cinnamon muffins! Your favorite flavors of fall in a healthy and delicious muffin.
Prep Time 15 minutes
Cook Time 20 minutes
Course Breakfast, Breakfast & Brunch, Dessert, Desserts, Snack, Snacks
Cuisine American
Servings 15 servings
Calories 220 kcal



  • 1 ¾ cup all purpose flour
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 1 tsp ground cinnamon
  • ½ tsp salt
  • 2 eggs
  • ½ cup non-fat Greek yogurt
  • ½ cup no sugar added applesauce
  • 2 tsp vanilla extract
  • 1 cup Crispy Green Freeze-Dried Apples approximately 3 single serving packages. Crushed or pulsed in food processor
  • ¼ cup light brown sugar
  • ¼ cup milk I used 2%
  • ½ cup extra virgin olive oil you can also use canola oil
  • 1 cup apples peeled and diced into ¼ in cubes

Crumble Topping

  • 2 tbsp cold butter
  • ¼ cup flour
  • 2 tbsp light brown sugar
  • ½ tsp cinnamon
  • ¼ cup Crispy Green Freeze-Dried Apples approximately one single serving package. Use food processor to crush.

Optional Cream Cheese Frosting

  • 2 oz light cream cheese
  • ½ tbsp butter
  • 2 tbsp milk I used 2%
  • 2 tbsp sugar
  • 2 tbsp Crispy Green Freeze-Dried Apples approximately ½ single serving package. Use food processor to crush.


  • Preheat oven to 425°F.
  • Spray muffin pans with nonstick spray or line with cupcake liners. You will need two pans as this recipe makes 15 muffins.

Crumb topping

  • Mix ingredients together in a medium bowl. Using a fork (or your hands if needed!), mix well until butter is smaller pieces. Set aside.


  • Whisk the flour, baking soda, baking powder, cinnamon, and salt together in a large bowl or the bowl for your mixer.
  • Add all the remaining ingredients EXCEPT the diced apple.
  • Mix well.
  • Mix until no flour pockets remain.
  • Fold in the apples.
  • Spoon the apple batter evenly into each cup, filling each all the way to the top.
  • Spoon crumb topping on each muffin, gently pressing it down so it sticks.
  • Bake for 5 minutes at 425° then, keeping the muffins in the oven, reduce the oven temperature to 350°F.
  • Bake for an additional 15 minutes or until a toothpick inserted in the center comes out clean.
  • Allow the muffins to cool before enjoying.

Cream Cheese Icing

  • Whisk all of the icing ingredients together. Place in the microwave for 30 seconds if needed to melt the butter.
  • Drizzle over warm or cooled muffins.


You will end up with leftover cream cheese icing! Save it, it will be good on just about everything.
Cover your muffins and keep them at room temperature for a few days or in the refrigerator for up to a week.
Nutrition facts will vary by the amount of cream cheese frosting added.


Calories: 220kcalCarbohydrates: 29gProtein: 4gFat: 10gSaturated Fat: 3gPolyunsaturated Fat: 1gMonounsaturated Fat: 6gTrans Fat: 0.1gCholesterol: 29mgSodium: 228mgPotassium: 120mgFiber: 2gSugar: 14gVitamin A: 118IUVitamin C: 1mgCalcium: 52mgIron: 1mg
Keyword apple, apple muffins, apple recipes, apples, healthy, healthy breakfast, healthy desserts, healthy snacks, muffins, snack
Tried this recipe?Let us know how it was!