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Hello! I’m Anjali. I’m a board certified health coach, author, wife, mom and food lover from the SF Bay area (now living in Seattle, WA!); with a passion for delicious food and a desire to make healthy eating easy, tasty and fun! Learn more about me here and stay for a while!

Anjali Shah

Healthy Apple Muffins Recipe with Cinnamon

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These healthy apple muffins are low calorie and are the perfect types of muffins for anyone– including kids! Made with sweet and fresh apples, carrots, warm cinnamon, unsweetened applesauce, and coconut sugar, this easy recipe is a great choice for breakfast, dessert, or even a mid-afternoon snack.

healthy apple muffins on a wire rack

Healthy with the most amazing sweet, yet tart flavor, this warm breakfast muffin recipe is loaded with nutrients and wholesome ingredients that are both comforting and indulgent. Moist and tender with a slight crunch from pecans, these healthy apple muffins are a great choice for almost any occasion any time of year!

Latest Recipe Video!

Easy to make gluten-free and vegan, these muffins contain no refined sugar and are great as lunchbox additions for toddlers, young kids, or even grown adults. When you bite into these muffins, you will immediately be met with a delicate balance of subtle sweetness and nuttiness from the coconut and apple flavor.

Exactly what you need for meal prep and when you’re looking to keep yummy treats in the house, these cinnamon apple muffins are satisfying without all the guilt!

Why You’ll Love This Recipe

  • Filled with Nutrients: A better choice than most muffins found in the grocery stores, these healthy apple muffins contain no added sugar, are nutrient-dense, and are loaded with fiber.
  • Made with Simple Ingredients: Made with basic pantry ingredients and some more easy ingredients, these low-calorie apple muffins are effortless!
  • Easy Recipe: This recipe for healthy carrot muffins is super easy to make, and also happens to be an easy grab and go breakfast or snack!
  • Great Option for Kids! This is one of my favorite healthy muffins recipes for kids! Kids think they are getting a delicious treat, while you can feel good about giving them a nutritious breakfast or snack!

How To Make The Best Healthy Apple Muffins

Ingredients and Notes

ingredients for healthy apple muffins

Dry Ingredients

Flour: We used a combination of all purpose flour and white whole wheat flour, but you can try almond flour, whole grain flour, oat flour, or coconut flour. You can use oat flour as a 1:1 substitution for the wheat flour in this recipe, but if you use almond or coconut you may need to add some xanthan gum to keep these healthy breakfast muffins light and fluffy.

Cinnamon: Warm ground cinnamon is used for this recipe to create a delightful balance of spicy and sweet. Apple and cinnamon? Yes, please!

Baking soda: Organic baking soda is used as a leavening agent for flour. Make sure you have this in your pantry!

Sea Salt: Your choice of Kosher sea salt for a nice well-rounded flavor.

Coconut sugar: We like to use coconut sugar as a refined sugar-free alternative to granulated white sugar. You can also substitute the coconut sugar for pure maple syrup or brown sugar.

Raisins: Either golden or purple raisins will work for this recipe.

Shredded coconut: Unsweetened shredded coconut for an extra nutty and moist flavors.

Pecans: A great source of healthy fats and protein, sweet and crunchy pecans are the perfect addition to these healthy muffins.

Wet Ingredients

Carrots: Grate your own carrots or buy shredded carrots from the store.

Apples: The options are limitless here for tart and sweet flavors! These muffins would be delicious with Granny Smith, Fuji, Pink Lady, or any other sweet apples that are in season! Make sure the apples are crisp.

Eggs: You will need eggs at room temperature for this recipe, but you can omit the eggs and use flax eggs instead!

Oil: Melted coconut oil or any other neutral oil.

Applesauce: Unsweetened apple sauce for additional moisture and apple flavors for these easy muffins.

Vanilla extract: We love to use pure vanilla extract for our baking recipes!

Step by Step Instructions

Read the recipe card for the full steps and details!

Preheat Oven

Prepare the Muffin Tin: First, preheat the oven temperature to 375 degrees Fahrenheit. Meanwhile, line the muffin tin with muffin cups or spray with cooking spray. Set aside.

muffin tin lined with muffin liners

Combine Ingredients

Sift Dry Ingredients: Next, in a large bowl, sift the flour with the ground cinnamon, salt, and baking soda. Then, stir in the sugar.

flour in a mixing bowl

Add the Shredded or Grated Apples: Next, fold in the carrots, grated apple, raisins, coconut, and pecans until combined.

carrots apples raisins coconuts pecans added to flour

Combine the Wet Ingredients: Next, whisk the eggs in a small bowl. Add the oil, eggs, and vanilla extract into the bowl with the eggs. Then make a well in your dry ingredients and add the egg mixture into the well.

well created in dough with eggs in the middle

Combine Wet and Dry Ingredients: Mix the eggs into the batter until just combined. Be careful not to overmix or you’ll end up with tough muffins!

wet and dry ingredients mixed in a bowl

Bake

Transfer Batter to Pan: Next, spoon the muffin batter into the prepared muffin pan.

batter in muffin tins about to go into the oven

Bake: Finally, transfer the tin to the preheated oven and bake muffins for 18-20 minutes, until the tops of the muffins are lightly golden brown. Place on a wire rack to cool slightly. Then, serve at room temperature.

healthy apple muffins in a muffin tin

Healthy Baking Substitutions

When you’re trying to make baked goods healthier, there are some easy substitutions you can make that will lighten up the recipe without sacrificing any of the flavor! Here are some of our favorites:

  • Instead of Cream: Use fat free half and half, or evaporated skim milk in a 1:1 ratio
  • Instead of Butter, Shortening or Oil to prevent sticking: Try olive oil cooking spray or baking spray
  • Instead of full fat cream cheese: Try low fat cream cheese or low fat cottage cheese pureed until smooth
  • Instead of Whole Eggs: Use two egg whites for each whole egg, or 1/4 cup egg substitute for each whole egg
  • Instead of All Purpose Flour: Use whole wheat pastry flour for half or all of the amount of all purpose flour called for in the recipe.
  • Instead of Canned Fruit: Use frozen fruit or fresh fruit
  • Instead of Whole Milk: Use 2% milk
  • Instead of Butter or Oil: You can reduce the amount of oil by 1/2 and add an equal portion of unsweetened applesauce
  • Instead of Full Fat Sour Cream: Try low fat sour cream or plain, low fat Greek yogurt
  • When A Recipe Calls For Sugar: Try reducing the amount of sugar needed by 1/2 and intensify the sweetness by adding a pinch of vanilla extract, nutmeg, cinnamon and / or other sweet spices

Recipe FAQs

What is the healthiest type of muffin?

The healthiest type of muffin is any muffin that is low in sugar (around 10-11 grams per muffin max), low in calories (less than 250 calories per muffin), made with real ingredients that are nutrient-dense and especially filled with protein. There are many types of healthy muffins out there, and this cinnamon apple muffin recipe is one of them!

What apples are best for muffins?

You want to make sure your apples are both tart, crisp, and sweet – and not too soft in texture (e.g. Golden Delicious apples would not work as well in these muffins). My favorite apples to use in muffins are Pink Lady, Fuji, and Granny Smith. If you want to get really creative, then you could even use a variety of apples.

What is the best breakfast for toddlers?

The best breakfast for toddlers would be anything that is well-rounded and filled with healthy ingredients! These healthy apple muffins are great for toddlers in addition to oatmeal, smoothies, fruit, gluten-free or whole grain waffles or toast, Greek yogurt, etc.

healthy apple muffins on a wire rack

Recipe Variations

Protein Muffins: Fold in some peanut or almond butter into this recipe for extra protein and fiber. These healthy apple cinnamon muffins are also great with peanut butter spread on the tops.

Blueberry Muffins: Instead of the raisins, use an equal amount of dried blueberries!

Spinach Muffins: Shred 1 cup of baby spinach and add it to the batter, reduce the amount of carrots by 1/2 a cup!

Pumpkin Muffins: Add 1/2 cup pumpkin puree to these healthy apple muffins, and reduce the applesauce by 1/2 a cup. Feel free to add 1/2-1 teaspoon of pumpkin pie spice and reduce the cinnamon by that same amount as well!

Healthy Banana Muffins: Add 1/2 cup banana puree and reduce the applesauce by 1/2 a cup. You could also use all banana puree and no applesauce (substitute in a 1:1 ratio)! You could also switch out the pecans for an equal amount of walnuts!

Vegan Muffins: Instead of the eggs, use flax eggs!

Gluten Free Apple Muffins: The easiest substitution to make these gluten free is to use gluten free oat flour instead of the regular flour. This will also turn these into a gluten-free apple oatmeal muffin recipe!

Expert Tips For These Healthy Apple Muffins

  • If using maple syrup instead of coconut sugar, then add it in with the other wet ingredients.
  • Store the muffins in an airtight container for up to 2-3 days at room temperature or 1 week in the fridge. To reheat, just warm slightly in the microwave.
  • Freeze these easy muffins by placing them in a freezer-safe container or bag and store in the freezer for up to six months. Then, allow the muffins to thaw in the refrigerator overnight, and then warm in the microwave or oven when ready to eat.
  • If you don’t have a hand grater to grate or shred the apples, carrots, etc. Then place carrots & apple chunks into a food processor and chop until grated.
  • To avoid ending up with a tough muffin, don’t overmix your batter. Just mix lightly until combined and then your batter is ready!
bite taken out of healthy apple muffins

More Healthy Breakfast Recipes!

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healthy apple muffins on a wire rack
Print Recipe
5 from 7 votes

Healthy Apple Muffins

These healthy apple muffins are low calorie and the perfect types of muffins for anyone– including kids! Made with sweet and fresh apples, carrots, warm cinnamon, unsweetened applesauce, and coconut sugar, this easy recipe is a great choice for breakfast, dessert, or even a mid-afternoon snack.
Prep Time15 mins
Cook Time20 mins
Total Time35 mins
Course: Breakfast
Cuisine: American
Servings: 20 large muffins
Calories: 230kcal
Author: Anjali Shah

Ingredients

  • 1 cup all purpose flour
  • 1 cup white whole wheat flour or whole wheat pastry flour
  • 2 teaspoons ground cinnamon
  • 2 teaspoons baking soda
  • ½ teaspoon salt
  • ½ cup coconut sugar or pure maple syrup
  • cups finely shredded carrots
  • 2 large tart apples, grated Pink Lady, Fuji, or Granny Smith
  • ½ cup raisins
  • ¾ cup shredded coconut
  • ½ cup chopped pecans
  • 3 lightly beaten eggs
  • ½ cup coconut oil
  • 1 cup + 1 Tbsp Unsweetened applesauce
  • ½ teaspoon vanilla extract

Instructions

  • Preheat oven to 375 degrees. Line muffin tins with baking cups; set aside.
  • Sift flour with cinnamon, baking soda, and salt into a large bowl. Stir in sugar until blended.
  • Then add carrots, apples, raisins, coconut, and pecans.
  • Stir mixture until combined.
  • Make a well in center of mixture and pour in eggs, oil, and vanilla all at once.
  • Stir just until mixture is evenly moist.
  • Spoon batter into muffin tins, filling at least ¾ full. Bake for 18 to 20 minutes or until golden. Serve warm.

Video

https://youtu.be/Y4PqGRxfpYw

Notes

Expert Tips  
  • If using maple syrup instead of coconut sugar, then add it in with the other wet ingredients.
  • Store the muffins in an airtight container for up to 2-3 days at room temperature or 1 week in the fridge. To reheat, just warm slightly in the microwave.
  • Freeze these easy muffins by placing them in a freezer-safe container or bag and store in the freezer for up to six months. Then, allow the muffins to thaw in the refrigerator overnight, and then warm in the microwave or oven when ready to eat.
  • If you don’t have a hand grater to grate or shred the apples, carrots, etc. Then place carrots & apple chunks into a food processor and chop until grated.
  • To avoid ending up with a tough muffin, don’t overmix your batter. Just mix lightly until combined and then your batter is ready!
Nutrition Facts lists 1 large muffin when making 20. Nutritional Information for 30 mini muffins (per muffin): 153 calories, 9.3g fat, 131mg sodium, 16.8g carbs, 2.5g fiber, 7.6g sugar, 2.1g protein

Nutrition

Serving: 1large muffin | Calories: 230kcal | Carbohydrates: 25.3g | Protein: 3.2g | Fat: 14g | Sodium: 197mg | Fiber: 3.7g | Sugar: 11g

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Whether it’s a quick smoothie or indulgent (but guilt-free) pancakes, my breakfast recipes have everything you need to start your day off right.

These recipes are healthy, filling, and easy to make!

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