Healthy Apple Muffins Recipe with Cinnamon and Whole Wheat Flour

These healthy apple muffins are the best apple cinnamon muffins thanks to whole ingredients, apple chunks, a fluffy texture, & flavorful honey. Seriously, this is a healthy apple muffin recipe that’s so good, my kids call them healthy apple cupcakes that don’t need frosting!

Healthy apple muffin on a plate with butter knife, tray of butter, and tin of muffins in the background

Are Muffins Healthy?

Breakfast muffins are a delightful treat, especially paired with a good cup of coffee. But not all muffins are created equal.

Take my recipe for the best blueberry muffins for instance. They’re absolutely amazing with a cinnamon streusel topping and a fluffy buttery crumb. They’re also 100% a dessert muffin.

Unlike our healthy apple muffins, most muffins you find in a coffee shop, bakery, or grocery store are made with processed ingredients. They don’t have much nutritional value, and in fact can contribute to diet related health problems.

Overhead of Healthy Apple Muffins in a muffin tin with orangey red towel

How do you make muffins healthy?

So how do you make muffins healthy? The easiest way is to use only whole ingredients. Think whole wheat flour, fresh produce, and natural sweeteners like honey or maple syrup.

You can also adapt them to certain dietary needs. These healthy apple muffins are dairy free because that is healthier for the dairy intolerant members of our family. We make our apple muffins with coconut oil instead of butter, and almond or coconut milk.

If you want to move beyond simply making clean eating apple muffins to lowering the fat content as well, you can even substitute apple sauce for the honey and coconut oil.

Baking tips

Before we jump into the recipe, here are a few baking tips to help you get the perfect muffin texture, and a way to make these healthy apple muffins even healthier!

Healthy apple cinnamon muffins with apple sauce

If you need to lower the carbohydrate, calorie, and fat content of these muffins, you can definitely substitute apple sauce for the honey and coconut oil.

There is a little wiggling of the recipe to make this work, since apple sauce has a higher water content than honey.

Healthy apple muffin torn in half to show chunks of apple and tender crumb texture

Normally you would use 1 cup of applesauce to replace 1 cup of honey and reduce the liquid ingredients by 2/3 cup.

But if you’re getting rid of the coconut oil already, you just need to reduce your milk by 1/3 cup.

So your liquid ingredients would now be 1 cup apple sauce, 1 egg, and 2/3 cup milk of your choice.

How to make vegan apple muffins

I have not tried swapping a chia seed slurry for the egg in this recipe. But if you follow the apple sauce substitution for the honey and oil, then use a vegan egg substitute, I’m guessing it would work.

If you try this I’d love to hear how it went!

How to measure flour

In our healthy apple muffins video, you’ll see that we pour the flour into the measuring cup and then scrape it level with the flat side of a knife. This is very important for getting an accurate dry ingredient ratio.

Toddler measuring flour with mom holding his hands

Scooping with the measuring cup can pack the flour in and increase your amount by as much as 50 %!

Use baking powder AND baking soda

You’ll also see in the cooking video below that I missed a key ingredient in making these healthy apple cinnamon muffins. You need both baking powder AND baking soda in the recipe. There is a difference.

Here are the muffins with just baking powder. See how flat and dense they are?

Flat Apple muffins in tin without baking soda for leavening

Baking soda reacts with acid in your ingredients to create carbon dioxide and causes your baked goods to rise. Baking powder contains both baking soda and an acid (usually cream of tartar), and sometimes cornstarch.

In some recipes (like these whole wheat apple muffins, which contain only a small amount of acid from the chopped apples) you need more leavening than can be provided by the acid in the recipe. That is why you need both baking powder AND baking soda.

Healthy Apple Muffins Recipe

See how much fluffier and lighter the muffin tops look with the added baking soda?

What kind of apples are best for baking?

There isn’t really a rule for what apples to bake with. But different apples do have different flavors, so that’s important to keep in mind. You do want to choose a firm apple though, so that the apple will hold its shape during cooking instead of turning to mush.

Here are our favorites for making these healthy apple muffins:

Honeycrisp

The Honeycrisp apple is the jack of all trades. It’s amazing eaten raw and in baked goods. These apples tend to be pricier, though we can get them for just 60 cents a pound at a local orchard in Washington!

Jonagold

I didn’t know about Jonagold apples until we started buying directly from a local orchard every fall. These apples have a great balance of tart and sweet, and have a yellowy green peel with a blush stripe.

Ripe red apples in burlap cloth on white table

Pink Lady

The Pink Lady is my go to apple for eating and baking. In these are exactly the apples I used to make these healthy apple muffins in the video. Pink ladies fall on the tart end of the spectrum, but still have a lot of sugar. They are incredibly crisp and have a lovely dark pink peel.

Granny Smith

Bright green Granny Smith apples are very tart and acidic, almost citrusy. This makes it a great option to balance out sweetness in baking.

How to make apple muffins

Here’s the video as promised! If you’re planning to make these healthy apple muffins for kids, you’ve got to see how much fun they can have helping you!

Ingredients

  • 2 cups white whole wheat flour
  • 1 1⁄2 teaspoons baking powder
  • 1 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 1⁄2 teaspoon salt
  • 1 cup honey
  • 1⁄3 cup melted coconut oil
  • 1 egg
  • 1 cup milk of your choice (dairy, almond, coconut)
  • 2 cups chopped apple (like Pink Lady or Honeycrisp)

Healthy apple and cinnamon muffins recipe steps

Combine first 5 ingredients in a large bowl and mix well. We use a fork to mix them.

Child Mixing dry ingredients in glass bowl for muffins

Stir in the liquid ingredients. I like to mix my wet ingredients together first, and then pour those into the dry ingredients.

Pouring honey into glass measuring cup of wet ingredients for apple muffins

It doesn’t make any extra dishes work if you use the liquid measuring cup you’d be measuring out your milk with.

Pouring wet ingredients into dry ingredients for baking muffins

Dump in the chopped apple. I like to leave the peels on, not just for the hint of color but also because they are full of nutrition.

Boy dumping chopped apples into bowl of muffin batter

Stir until apples are just mixed in.

Woman's hands mixing apple muffin batter in a glass bowl

Spoon into greased muffin tin about 3/4 full.

Muffin tin filled with apple muffin batter

Bake at 400F for 25-30 minutes, until golden brown and toothpick inserted comes out clean.

Healthy Apple Muffins in a tin and on a plate

How to store apple muffins

If you are planning to eat these healthy apple muffins within a few days you can just leave them on the counter. If you need them to last a week, store them in the fridge.

A sealed container will help keep them from getting dry, though here in the Seattle area we don’t have to worry about that as much!

Can you freeze apple muffins?

You can also freeze this healthy apple muffin recipe. Place them in a resealable plastic bag or an airtight food storage container in your freezer.

To defrost, place the muffin in the fridge overnight, or microwave for 60-90 seconds.

You can even place a frozen muffin in your kiddo’s lunchbox and it should be soft enough to eat by lunchtime!

Pin to save this easy apple muffin recipe!

Don’t lose this recipe! Save the image below on Pinterest and then leave a photo in the comments of the pin once you’ve made it. We love seeing your creations!

Healthy Apple Muffins text with photos of muffins
Save on Pinterest

What to serve with muffins for breakfast

Thanks to the whole wheat and coconut oil in these healthy apple muffins, you get longer lasting energy than you would from regular muffins. But if you are a big breakfast eater, I suggest pairing them with eggs for some more protein.

Try scrambled eggs or add some veggies and protein serving them with naturally green eggs and ham. If you’re eating on the go, you could pair them with boiled eggs, a frozen breakfast burrito, microwave omelet in a jar, or even a SPAM musubi!

If you aren’t an egg person, you might like them with these sausage and cheese breakfast quesadillas from my friend Kalyn!

Printable healthy apple muffins recipe

Yield: 12 muffins

Healthy Apple Muffins with Cinnamon

Healthy Apple Muffins in a tin and on a plate

These healthy apple muffins are the best apple cinnamon muffins thanks to whole ingredients, apple chunks, a fluffy texture, & flavorful honey.

Ingredients

  • 2 cups white whole wheat flour
  • 1 1⁄2 teaspoons baking powder
  • 1 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 1⁄2 teaspoon salt
  • 1 cup honey
  • 1⁄3 cup melted coconut oil
  • 1 egg
  • 1 cup milk of your choice (dairy, almond, coconut)
  • 2 cups chopped apple

Instructions

  1. Combine first 5 ingredients in a large bowl and mix well.
  2. Stir in the liquids and then the chopped apple.
  3. Spoon into greased muffin tin about 3/4 full.
  4. Bake at 400F for 25-30 minutes, until golden brown and toothpick inserted comes out clean.
  5. Let cool in the pan for 10 minutes, then remove to cool completely.

Nutrition Information:

Yield:

12

Serving Size:

1

Amount Per Serving: Calories: 235Total Fat: 7gSaturated Fat: 5gTrans Fat: 0gUnsaturated Fat: 1gCholesterol: 17mgSodium: 272mgCarbohydrates: 42gFiber: 3gSugar: 25gProtein: 4g

Nutrition information is an estimate only.


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