These healthy apple cinnamon muffins are sweet and crunchy thanks to a streusel topping, and packed with nutritious carrots and zucchini. Make a double batch and enjoy one now, and save one for breakfast or snacks the next day!

The air is crisp and the winds are strong. The boots and sweaters are out. It's definitely fall here in the Pacific Northwest, and for me that means apples and baked goods!
I love cooking with apples and baking with them! They enhance fall dishes like Pork Tenderloin with Hard Cider, Apples, and Sage or Roasted Brussels Sprouts. And they are perfect for delicious treats like Apple Pie Bars, Skillet Apple Crisp, Baked Apple Cinnamon Donuts, and Apple Fritters.
We had so many apples from my recent trip with Travel Oregon to Kiyowaka Family Orchards. So I decided to make healthy apple cinnamon muffins.
What you need to make apple cinnamon muffins

These delectable muffins are packed with healthy fruits and vegetables. The full ingredient measurements are in the printable recipe card below. To start, you'll need:
- green apples
- carrots
- zucchini
- all-purpose flour
- granulated sugar
- light brown sugar
- baking soda
- baking powder
- vanilla extract
- large eggs
- almond milk
- ground cinnamon
- butter

A super buttery, sugary streusel topping for these apple muffins that would probably negate the healthy addition of the veggies... but totally make each and every bite of these muffins THE BEST HEALTHY APPLE CINNAMON MUFFINS you have ever tasted.
My 12-year-old son declared these muffins to be the best I have ever made.
My 9-year-old daughter couldn't get enough.
Then I told them they had veggies in them. Their smiles turned to small frowns... and then the little rascals shrugged and continued to eat more. And more. My son even commented "I can't even tell there are veggies in here." That's the beauty of these, son. Enjoy!
Fair warning: you should most definitely double this recipe and make two batches, because they will be gone so fast!
Tips for baking the best apple cinnamon muffins

There are two secret ingredients that make these healthy apple cinnamon muffins so soft and tender. It's thanks to the added moisture from the grated carrots and zucchini. I use finely grated – not shredded veggies – because that helps bring out the liquids in the veggies and helps them blend in more in the muffins.
Another trick: dice the apples into teeny tiny itty bitty little pieces (see the photo with ingredients above). This helps the muffins to cook evenly. Not to mention, many people don't like biting into large chunks of fruit in muffins.
One additional trick: add some of the itty bitty apple pieces to the buttery sugary streusel topping. This gives these muffins the most delicious, satisfying crunch to each and every bite.

How to store muffins

Store baked muffins in an airtight container at room temperature for up to five days. You can also freeze them in freezer-safe containers for up to two months.

If you would like to make these even healthier, simply omit the streusel topping. I mean, they are really good without the topping, but they are oh so better with the topping!

We're making these all the time now. We made these last weekend. I'm making them every chance I get. Try the recipe for yourself and let me know how yours turn out!

Healthy Apple Cinnamon Muffin Recipe (with veggies)
Ingredients
Muffins
- 8 tablespoons 1 stick butter at room temperature
- ½ cup granulated sugar
- ½ cup brown sugar
- 2 eggs
- 1 teaspoon vanilla
- ½ cup almond milk
- ½ cup peeled finely diced green apples
- ¼ cup finely grated carrots
- ¼ cup finely grated zucchini
- 2 cups all-purpose flour
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ½ teaspoon ground cinnamon
Streusel Topping
- ⅔ cup all purpose flour
- ¼ cup brown sugar
- ¼ cup granulated sugar
- ¼ teaspoon ground cinnamon
- ¼ cup finely diced itty bitty pieces of green apple
- 6 tablespoons cold butter cut into small cubes
Instructions
- Pre-heat oven to 375 degrees.
- Prepare a 12-cup muffin tin with muffin/cupcake liners. Set aside.
To Make The Streusel Topping
- In a medium or large bowl, sift together flour, brown sugar, granulated sugar, ground cinnamon, and green apple until well blended.
- Using your hands (or two forks, but your hands are the best kitchen tools for this job!), add the cubes of butter and knead them into the dry mixture until you get a nice crumble (see photo on UrbanBlissLife.com for example).
- Set aside.
To Make Muffins
- In a stand mixer or using a hand mixer over a large bowl, cream the butter and both sugars until well blended. Slowly add the eggs and vanilla, then the almond milk.
- With the mixer on slow speed, gently add the green apples, carrots, and zucchini. Mix for 1-2 minutes until well blended.
- While the wet ingredients are mixing, in a separate, large bowl, sift together the flour, baking powder, baking soda, salt, and ground cinnamon.
- Slowly add the dry ingredients to the wet ingredients until well blended.
- Using a medium cookie scooper or spoon, fill muffin cups about ¾ of the way.
- Top each muffin cup with enough streusel to cover the top of the muffin batter.
- Bake at 375 degrees for 22-25 minutes. Tops should be golden brown.
Notes
Nutrition
Nutrition information is a general estimate. Actual nutrition details may vary depending on the exact foods & brands you use to make this recipe. It does not take into account any substitutions, toppings, or optional ingredients.

What are your favorite fall baked goods to enjoy when the weather turns crisp and cool?
Kristina says
We are a vegan family. What can I sub for the eggs in this recipe? The rest of substitutions I have already worked out. Thanks for your help.. Hoping I get to make these vegan style with your recommendation!
Marlynn Jayme Schotland says
Two of the more typical substitutions I've heard people use in baking are mashed banana and silken tofu. I have not tried any egg substitutions in this particular recipe, so I can't tell you how it will turn out. If you do try it, however, please do let me know how it goes and which substitution you used. Thanks, Kristina!
Mama Munchkin (@globalmunchkins) says
I cannot wait to bake these muffins. My 3 year old is the world's pickiest eater so I have to get creative. I haven't tried muffins yet but I bet if I get the veggies and apples chopped super fine she will have NO IDEA the muffins are healthy ;) Thanks for the recipe!!
Marlynn Jayme Schotland says
Muffins are a great go-to for sneaking in veggies for picky eaters - I've had a lot of experience with those in my house as well ;) Thanks so much!
Mary says
I ended up making them over the weekend! I did make a few changes. The main change was that I did go ahead and try the whole wheat flour. I also added a couple tablespoons of apple sauce to try to add more moisture, fearing the whole wheat would make them too dry. It worked. They were still a touch more dry than I'd like (but hey, whole wheat!). But overall the flavors were great! I also cut back on the sugar and used 1/2 cup of maple syrup instead (and just a couple tablespoons of sugar), because I'm a nut and trying to reduce sugar for my kids snacks. Again, they still turned out great! My husband is the biggest judge when it comes to me trying to make "healthy" muffins and snacks, and he gave it 2 thumbs up!
Oh, I kept the streusel exactly as you suggested (I did use white flour for that).
Not sure if it was from my changes/additions, but the mix did make a lot more than 12 regular size muffins... but that just meant we got to make a small batch of mini-muffins too!! Bonus!!
Thanks for this recipe. We'll definitely be making it again.
Marlynn Jayme Schotland says
Great to hear! Thanks for trying them out, and so glad you liked them, Mary!
Megan says
I wonder if these will freeze well - I love having a stash of muffins ready to go!
Lynn says
I love the "sneaky" way it's mixed with vegetables. I wouldn't object too much if my kids will reach for one for snack because I know that apart from looking this yummy, they have nutrients too!
Aileen says
It's still hot here in Northern California, but I am ready for the cool Fall weather. These muffins look delicious!
Amanda says
These look great! I don't do a ton of baking with zucchini, but I love how it's folded and hidden in here with yummy fall flavors... secret hidden vitamins for the win!
Bella says
These look so good. I love apple muffins they are my fav. I will have try this recipe.
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