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These healthy Apple Cinnamon Muffins are made with almond flour, coconut flour, egg whites, freshly diced apple, and warm cinnamon, delivering all your favorite fall flavors. They’re naturally gluten-free and dairy-free, about 272 calories each with 8 grams of protein and 5 grams of fiber.

Apple cinnamon muffins on a plate.
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Quick Summary: Apple Cinnamon Muffins

  • Why Make This Recipe: These fluffy apple cinnamon muffins are full of fresh apple and apple pie flavor. They make the perfect portion-controlled fall snack or dessert.
  • Nutrition: 272 calories, 8 grams of protein, 5 grams of fiber
  • Diet: Low-Calorie, Gluten-Free, Dairy-Free, Paleo
  • Time: Prep Time = 10 minutes, Bake Time = 30 minutes, Total Time = 40 minutes
  • Method: Baked
  • Best for: A delicious breakfast or snack on the go that’s easy to make ahead and freeze.
  • Tip: The batter for these muffins should be thick because it helps the apples not sink to the bottom. 

These low-calorie apple muffins with almond flour are the perfect replacement for bakery muffins. They are moist and bursting with flavor, but have a fraction of the sugar and calories.

\Many bakery muffins have 300-400 calories, whereas these only have 272 calories and are sweetened with just 2 tablespoons of honey. Plus, these muffins have protein and fiber to help you feel satisfied and to fuel your day.

If you like easy apple breakfast recipes, you will love my healthy apple pancakes and apple and Brussels sprouts breakfast hash.

Why You’ll Love This Recipe

  • Packed with Protein: Almond flour has more protein than regular flour, so paired with the egg whites, it packs 8 grams of protein into each muffin.
  • One Whisk, Two Bowls, No Mixer: There’s no need for stand mixers or electric mixers with these muffins. The batter comes together in two bowls using a whisk and then a spoon.
  • Freezer-Friendly: Store your muffins in the freezer for up to 3 months for a perfectly portioned breakfast or snack anytime. 

Ingredients

Ingredients to make these healthy apple muffins in bowls on a table.
  • Apples: Use firm, sweet-tart apples such as Honeycrisp, Pink Lady, Gala, or Granny Smith apples because they will keep their shape and the flavor stands out.
  • Egg Whites: Use room-temperature egg whites, which are full of protein but contain less fat and calories than whole eggs. 
  • Honey: These muffins are naturally sweetened with honey, but you can use maple syrup instead. 
  • Almond Flour: Almond flour is high in natural fats and oils to make the muffins more moist. It also contains protein and fiber. 
  • Coconut Flour: Coconut flour is very absorbent, which helps balance the excess fats and oils in almond flour. It is also packed with fiber.

See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.

Variations & Dietary Modifications

  • Add Nuts, Berries, or Veggies: Give your muffins a little crunch by mixing in chopped walnuts or pecans. You could also add blueberries, raisins, or even veggies, like in my apple and carrot muffins.
  • Swap for Pears: Apples are a popular fruit for fall, but pears are just as delicious! 
  • More Spices: This recipe just calls for cinnamon, but you can bring out more robust fall flavors by also adding nutmeg and cloves or a prepackaged apple pie spice.
  • Use Whole Eggs: Instead of egg whites, you can use whole eggs for these muffins. Just keep in mind that this will change the calories and fat content.

How to Make Apple Cinnamon Muffins

There’s just something comforting about a warm, cinnamon-packed muffin bursting with natural sweetness and nutty goodness. They come together without an electric mixer, just a whisk, a spoon, and two bowls. You’ll also need to preheat your oven to 350°F and use muffin liners or grease your muffin tin with cooking spray.

The dry ingredients mixed together in a bowl.
  1. Step 1: Mix Dry Ingredients. Combine the almond flour, coconut flour, baking soda, cinnamon, and salt in a medium bowl using a whisk. 
Egg whites, honey and oil mixed together in a bowl.
  1. Step 2: Whisk Wet Ingredients. In a separate bowl, whisk together the egg whites, honey, and olive oil.
The wet and dry ingredients combined.
  1. Step 3: Combine Wet and Dry. Fold the dry ingredients into the wet ingredients and stir until they are just combined. Then add the chopped apples.
The muffin batter put into muffin liners.
  1. Step 4: Scoop and Bake. Scoop the batter into the muffin tins until they are ¾ full. Use your finger to smooth the edges of the muffins. Bake them for 22-25 minutes at 350°F until they are golden brown. Then remove from the oven and let cool for 5-10 minutes before transferring to a wire rack to cool completely.

Expert Tips

  • Thick, Scoopable Batter: This batter is very thick and easy to scoop. It’s ideal because it prevents the apple chunks from sinking to the bottom of the muffins.
  • Measure Flour Properly: It’s important to properly measure the flour when baking with gluten-free flour. Scooping it directly with a measuring cup may cause you to use too much flour, which will make your muffins dry and dense. 
  • Create a Dome: Create the perfect round dome on the top of the muffins by running your finger around the edge of the muffin liner. This slightly pushes the batter to the middle of the muffin.
  • Storing: Keep muffins in an airtight container on the counter for 1-2 days, or in the refrigerator for 5 days. You can freeze the paleo apple muffins for up to 3 months.
An apple muffin with a bite taken out of it.

Serving Suggestions

If you love apple desserts, like apple pie or apple crisp, you’ll love these gluten-free apple muffins! They are bursting with cinnamon and fresh apple chunks, but are also full of fiber and protein to help keep you feeling satisfied. They make a great dessert or breakfast for Thanksgiving, but you can enjoy them all year round as well. 

Apple Cinnamon Muffins Recipe FAQs

Do I need to peel the apples to make apple cinnamon muffins?

No, you don’t need to peel the apples. The apple skins are loaded with fiber, so it’s best to leave them on.

Can I use applesauce instead of chopped apples in these cinnamon apple muffins?

No, applesauce cannot be used as a substitute because it adds too much moisture to the batter, and the flour measurements don’t accommodate it. 

Can I use regular or oat flour instead of almond and coconut flour?

No. This recipe was made for almond and coconut flour, and other gluten-free flours will not work with it as is. If you’d rather make apple muffins with oat flour, try my healthy apple muffins with oats recipe instead.

A bunch of apple muffins on a wire rack.

More Healthy Apple Dessert Recipes

If you tried this Apple Cinnamon Muffins recipe or any other recipe on my website, please leave a 🌟 star rating and let me know how you go in the 📝 comments below.

A plate filled with apple cinnamon muffins.
5 from 1 vote
Servings: 10 muffins

Apple Cinnamon Muffins

Make apple cinnamon muffins using a whisk and two bowls in just 25 minutes for an easy low-calorie breakfast or dessert.
Prep: 10 minutes
Cook: 30 minutes
Total: 40 minutes
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Ingredients 

  • Âľ cup Red Apples, peeled, cored and diced finely
  • ½ cup Olive Oil, or oil of choice
  • 6 large Egg Whites
  • 2 tablespoons Honey
  • 2 cups Almond Flour
  • 6 tablespoons Coconut Flour
  • 1 teaspoon Baking Soda
  • 2 tablespoons Cinnamon

Instructions 

  • Preheat oven 350 F. Prepare a muffing tin with muffin liners or cooking spray.
  • In a medium bowl, mix together the dry ingredients until broken down and incorporated well.
  • In a separate large bowl, whisk together egg whites, honey and oil.
  • Fold the dry ingredients into the wet ingredients and stir just until combined. Do NOT over stir. Coconut flour is very absorbent so you want to gently fold the ingredients together. Gently fold in the chopped apples.
  • Scoop the batter into the muffin cavities filling 3/4 of the way full. I used my finger to smooth the edges so the muffins would puff nicely.
  • Bake 22-25 minutes until muffins are golden brown. Remove from the oven and transfer to a wire baking rack to cool 5-10 minutes before removing and enjoying.

Notes

  • Measure the flours by spooning them into the measuring cup rather than scooping them directly and packing in the flour. Too much flour will dry out the muffins.
  • The batter should be thick and scoopable, not drippy. This will help hold the apples in place to avoid them sinking to the bottom of the muffins.
  • Use your finger to smooth along the edge of the muffin cups. This will help create a round dome at the top of the muffins.

Nutrition

Serving: 1muffin, Calories: 272kcal, Carbohydrates: 13g, Protein: 8g, Fat: 23g, Saturated Fat: 3g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 8g, Sodium: 152mg, Potassium: 51mg, Fiber: 5g, Sugar: 6g, Vitamin A: 10IU, Vitamin C: 1mg, Calcium: 65mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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Megan

Megan is a nutritionist who coaches women 35+ lose weight sustainably. She is the author of the Low Calorie Cookbook, fitness instructor, host of the Dish On Ditching Diets Podcast and creator of Skinny Fitalicious where you get lighter, higher protein recipes. Follow Megan on Facebook, Pinterest, YouTube and Instagram for the latest updates.

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8 Comments

  1. Laura @ Sprint 2 the Table says:

    These look fabulous! I love almond meal baked goods. Such a fabulous texture!

    1. Megan says:

      Thank you! Hope you get to try them.

  2. Blair says:

    Oh yum! I bet the house smells amazing while these bake!

    And I agree — actions speak louder than words. I’d devour these (that’s an action, right)?! 🙂

    Glad to see another delicious muffin recipe back on the blog!

    1. Megan says:

      That’s a good action! Muffins have been a little MIA lately. I need to get on them.

  3. Jody - Fit at 58 says:

    YUMMMMMMMMMMMMMMMMMMMMMMM

    1. Megan says:

      Thank you!

  4. Kristen says:

    These sound delish and super easy! Making them soon! =)

    1. Megan says:

      Awesome, hope you like them!