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Healthy Apple Muffins

Amazing, healthy apple muffins made with maple syrup and whole wheat flour! No one will guess that this simple cinnamon apple muffin recipe is healthy, too.

Updated by Kathryne Taylor on August 30, 2024

692 Reviews

1823CommentsJump to recipe

It’s apple muffin time! You all really seem to love my banana muffins, pumpkin muffins and carrot muffins and the blueberry muffins in my cookbook. Today, apple muffins are joining the club.

Like the others in the bunch, these muffins are made with 100 percent whole wheat flour and naturally sweetened with maple syrup or honey. They are nice and fluffy, with just enough sweetness to be irresistible.

Granted, I already have an apple oatmeal muffin recipe on the blog from four years ago, but I have significantly upped my muffin game since then. These muffins are the better of the two, by a long shot.

I based these healthy apple muffins off my carrot muffins, replacing grated carrots with fresh apple, and replacing half of the Greek yogurt with applesauce.

These muffins contain apple, three ways: freshly grated and chopped apple for the perfect texture, and applesauce for infused apple flavor. They’re the best apple muffins I’ve ever had.

Healthy Apple Muffin Notes

• These apple muffins taste even better after resting for a few hours, if they last that long.
• I particularly enjoy them with a spread of peanut butter.
• Check my recipe notes for how to use honey instead of maple syrup, and some ideas for how to make the muffins vegan.

I think it’s time for another! Please let me know how you like these muffins in the comments. I love hearing from you.

Baking Tips for Success

How to Measure Flour

How you measure your flour is important. Why? If you measure incorrectly, you could end up with up to 50 percent extra flour, which will make your muffins dense, dry and flavorless. Use the spoon and swoop method:

1. Gently stir your flour to loosen any clumps.
2. Spoon your flour into the measuring cup with a big spoon or a flour scoop. Do not scoop up the flour directly into the measuring cup.
3. Level off the top of the cup with a knife. Repeat as necessary.

Baking Powder & Baking Soda Are Not the Same Thing

…and they are not interchangeable. Both are leaveners that help your baked goods rise (baking powder contains some baking soda, but that’s a long story).

This recipe relies on a combination of baking powder and baking soda to produce light and fluffy muffins. For ideal results, always follow the recipe and measure carefully.

How to Stir Your Batter

This muffin batter is super simple to stir together by hand, and that’s how I recommend making these muffins. Why? Whipping your batter will make the flour’s gluten protein too strong, yielding tough muffins.

I know it can be tempting to use a stand mixer or hand mixer when it’s within reach. Please don’t! Follow the instructions below and you’ll end up with light, fluffy muffins.

Watch How to Make Apple Muffins

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Healthy Apple Muffins

• Author: Cookie and Kate
• Prep Time: 15 mins
• Cook Time: 13 mins
• Total Time: 28 minutes
• Yield: 12 muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.8 from 692 reviews

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Amazing, healthy apple muffins made with maple syrup and whole wheat flour! No one will guess that this simple cinnamon apple muffin recipe is good for you, too. Recipe yields 12 muffins.

Ingredients

• 1 ¾ cups white whole wheat flour or regular whole wheat flour
• 1 ½ teaspoons baking powder
• 1 teaspoon ground cinnamon
• ½ teaspoon baking soda
• ½ teaspoon salt
• 1 cup grated apple
• 1 cup apple diced into ¼” cubes
• ⅓ cup melted coconut oil or extra-virgin olive oil
• ½ cup maple syrup or honey*
• 2 eggs, preferably at room temperature
• ½ cup plain Greek yogurt (I used full-fat but any variety should do)
• ½ cup applesauce
• 1 teaspoon vanilla extract
• 1 tablespoon turbinado sugar (also called raw sugar), for sprinkling on top

Instructions

1. Preheat oven to 425 degrees Fahrenheit. If necessary, grease all 12 cups on your muffin tin with butter or non-stick cooking spray (my pan is non-stick and doesn’t require any grease).
2. In a large mixing bowl, combine the flour, baking powder, cinnamon, baking soda and salt. Blend well with a whisk. Add the grated apple (if it is dripping wet, gently squeeze it over the sink to release some extra moisture) and chopped apple. Stir to combine.
3. In a medium mixing bowl, combine the oil and maple syrup and beat together with a whisk. Add the eggs and beat well, then add the yogurt, applesauce and vanilla and mix well. (If the coconut oil solidifies in contact with cold ingredients, gently warm the mixture in the microwave in 30 second bursts.)
4. Pour the wet ingredients into the dry and mix with a big spoon, just until combined (a few lumps are ok). The batter will be thick, but don’t worry! Divide the batter evenly between the 12 muffin cups. Sprinkle the tops of the muffins with turbinado sugar. Bake muffins for 13 to 16 minutes, or until the muffins are golden on top and a toothpick inserted into a muffin comes out clean.
5. Place the muffin tin on a cooling rack to cool. If you have leftover muffins, store them, covered, at room temperature for up to 2 days, or in the refrigerator for up to 4 days. Freeze leftover muffins for up to 3 months.

Notes

Recipe adapted from my healthy carrot muffins.

*If you are baking with honey: Honey tends to brown quickly, so to avoid overdone muffins, bake muffins at 325 degrees Fahrenheit until a toothpick inserted in the center comes out clean, about 23 to 25 minutes.

Make it vegan: Replace the eggs with flax eggs and replace the yogurt with vegan buttermilk—try mixing 1 ½ teaspoons vinegar with a scant ½ cup non-dairy milk. Let it rest for 5 minutes before adding it to the other liquid ingredients. (You could also try using more applesauce in place of the yogurt but I’m not sure it’s acidic enough to counteract the bitter taste of the baking soda.)

Make it dairy free: See “buttermilk” option above.

Make it egg free: Use flax eggs instead of regular eggs.

Make it gluten free: Bob’s Red Mill or King Arthur Flour make gluten-free all-purpose blends that work well.

Nutrition

The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice. See our full nutrition disclosure here.

• Category: Muffins
• Method: Baked
• Cuisine: American