Healthy Apple Carrot Muffins

This post may contain affiliate links. As an Amazon Associate, I earn from qualifying purchases. Please read my disclosure.

These healthy apple carrot muffins are low calorie and are one of our favorite muffin recipes for a recipe! These sunshine muffins are fantastic for the whole family. They are 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 with the most amazing sweet, yet tart flavor, this healthy carrot muffin recipe is loaded with nutrients and wholesome ingredients that are both comforting and indulgent. Moist and tender with a slight crunch from pecans and warm cinnamon flavor, these carrot apple muffins are a great choice for almost any occasion any time of year!

Easy to make gluten-free and vegan, these wholesome muffins contain no refined sugar and are a great recipe to use as lunchbox additions for toddlers, young kids, or even grown adults. When you bite into an apple carrot muffin, you will immediately be met with a delicate balance of subtle sweetness and nuttiness from the coconut and apple flavor. They taste like a healthy carrot cake muffin enhanced with apple cinnamon flavor – simply divine!

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

👩🏽‍🍳 Why You’ll Love This Healthy Apple Carrot Muffin Recipe

• Filled With Nutrients: Also known as superhero muffins because of how nutritious and filling they are, these healthy apple muffins are a better choice than most muffins found in grocery stores. They contain no refined sugar, are nutrient-dense and chockful of whole grains, and are loaded with fiber.
• Made With Simple Ingredients: Made with basic pantry ingredients and some more easy ingredients, this delicious muffin recipe is effortless!
• Easy Recipe: This recipe for healthy carrot cake muffins is super easy to make, and also happens to be a quick breakfast or healthy snack!
• Great Option For Kids! This is one of my favorite healthy muffins recipes for kids, and they’re a great way to sneak in some veggies at breakfast time. Kids love them because they are tasty and sweet, while you can feel good about giving them a nutritious breakfast or snack!

Latest Recipe Video!

🥘 Ingredients

Make these sweet apple carrot raisin muffins with common and healthy ingredients found at almost any grocery store!

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

• Flour: I used a combination of all-purpose flour and white whole wheat flour for added whole grains and a great texture.
• Cinnamon: Warm ground cinnamon is used for this recipe to create a delightful balance of spicy and sweet. Apple and cinnamon flavor? Yes, please!
• Baking Soda: Leavens the batter, producing the best fluffy muffins!
• Sea Salt: Choose Kosher sea salt to enhance the muffin flavor.
• Coconut Sugar: A healthier alternative to white sugar, coconut sugar adds warm and molasses-like notes to these healthy apple muffins without refined sugar. You can also substitute the coconut sugar for pure maple syrup or brown sugar.
• Raisins: Choose classic purple raisins or golden raisins for this morning glory muffin recipe.
• Shredded Coconut: Opt for unsweetened shredded coconut to keep these carrot breakfast muffins refined sugar-free.
• Pecans: A great source of healthy fats and protein, sweet and crunchy pecans are the perfect addition.
• Carrots: Grate your own carrots using a box grater or food processor fitted with the grating attachment or buy pre-shredded carrots from the store.
• Apples: The options are limitless here for tart and sweet flavors! I used Granny Smith, but any type of apple will work (see below for substitutions!)
• Eggs: Bring the eggs to room temperature before making this apple carrot raisin muffins recipe. To do so quickly, place the eggs in lukewarm water for 5 minutes.
• Oil: Choose melted coconut oil or another neutral oil like vegetable, grapeseed, or even avocado 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!

🍲 Ingredient Substitutions

• Flour: Instead of white whole wheat flour you can also use whole wheat pastry flour. These muffins can also be made with almond 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 the muffins light and fluffy.
• Apples: These apple carrot and raisin muffins would be delicious with Granny Smith, Fuji, Pink Lady, or any other sweet apples that are in season! Make sure the apples are fresh, juicy, and crisp.
• Nuts: If you don’t have pecans, walnuts or slivered almonds will also work!
• Extract: You can use almond extract if you don’t have vanilla!
• Applesauce: Mashed bananas will also work in place of applesauce, so will pureed pears.

🔪 How To Make Healthy Apple Carrot Muffins

Make these healthy carrot raisin muffins in just a few simple steps. Here’s how:

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

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

Stir In Apples, Carrots, And Raisins: Fold the grated carrots, grated apple, raisins, coconut flakes, and pecans into the flour mixture until combined.

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

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!

Transfer Muffin Batter To The Muffin Pan: Next, spoon the muffin batter into the prepared muffin cups, spooning an equal amount into each.

Bake The Muffins: Finally, transfer the tin to the preheated oven and bake muffins for 18-20 minutes, until the muffins are lightly golden brown. Place on a wire rack to cool to room temperature before serving. Enjoy these fresh muffins immediately!

💭 Expert Tips

• Make Mini Muffins: Make mini healthy carrot apple muffins by using a mini muffin pan. Scoop 2-3 tablespoons of muffin batter into the prepared pan and bake for 11-13 minutes, or until a toothpick inserted in the center of the muffins comes out clean.
• Muffin Liner Options: Use paper liners or even silicone muffin liners for easy serving. Otherwise, just spray the muffin tin with non-stick cooking spray before filling with the muffin batter.
• Maple Syrup Adjustments: If using maple syrup instead of coconut sugar, then add it in with the other wet ingredients.
• Don’t Overmix The Batter: To avoid ending up with a tough muffin, don’t overmix your batter. Just mix lightly until combined and then your batter is ready!

📖 Variations

• Protein Muffins: Whisk 2-3 tablespoons of some peanut or almond butter in with the wet ingredients to add extra protein and fiber to these delicious apple carrot muffins. You can also stir a scoop or two of protein powder in with the dry ingredients.
• Blueberry Muffins: Instead of the raisins, use an equal amount of dried blueberries!
• Carrot Apple Zucchini Muffins: Add 1 cup of shredded zucchini to the batter and reduce the amount of carrots by 1/2 a cup! You can also experiment with other shredded veggies like sweet potato, butternut squash or even parsnips!
• Sweeter Muffin: These carrot apple raisin muffins are naturally sweet, but if you really want to satisfy your sweet tooth and go for more of a dessert like feel, add 1/2 cup dark chocolate chips into the batter and top with additional chocolate chips!
• Pumpkin Muffins: Add 1/2 cup pumpkin puree to these healthy carrot 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 Carrot Muffins: Add 1/2 cup mashed ripe banana 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!

🍽 Serving Suggestions

Serve healthy apple carrot muffins with a glass of hot tea, freshly brewed coffee, or a glass of orange juice for a light breakfast. They’re also delicious toasted or warmed in the microwave and spread with peanut butter, vegan nutella, vegan butter, or coconut oil.

Make a more satisfying breakfast or snack by serving the muffins with fresh fruit or this breakfast fruit salad, pumpkin yogurt parfaits, or with a healthy kale smoothie.

🙌 Dietary Adaptations

As written, this carrot muffin recipe is naturally healthy, dairy-free, and vegetarian! To make it vegan and gluten-free, just make the following easy adaptations:

• Vegan: To make plant-based carrot muffins, just substitute flax eggs for regular eggs.
• Gluten-Free: To make gluten-free carrot muffins, just substitute oat flour for the regular flour in a 1-to-1 ratio.
• No Sugar Apple Muffins: To make these muffins without any added sugar, omit the coconut sugar or use monk fruit or stevia as an alternative.

🫙 Storage Directions

• Storing: Store these low calorie muffins in an airtight container for up to 2-3 days at room temperature or 1 week in the fridge.
• Freezing: Freeze the muffins in a freezer-safe bag for up to 6 months. Defrost the muffins at room temperature for 20-30 minutes before enjoying.

❓Recipe FAQs

🧇 More Healthy Breakfast Recipes!

• Vegan Breakfast Cookies
• Sourdough Croissants
• Savory Veggie Muffins
• Healthy Cranberry Orange Muffins
• Birthday Cake Muffins
• Dairy-Free Blueberry Muffins
• Spicy Oatmeal Recipe
• Cinnamon Streusel Muffins
• Banana Bread Without Butter
• Vegetarian Breakfast Ideas

📋 Recipe Card