Return to top
featured in… The Huffington Post CookingLight Reader's Digest Women's Health BuzzFeed Glamour Whole Foods Oprah Winfrey Network CNN Food Network Healthline Shape

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 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.

Overhead shot of a small wire rack of healthy apple muffins with raisins, coconut, and a dish towel.

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.

All of the ingredients for healthy apple carrot muffins on the counter.
  • 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.

Overhead shot of a muffin tin lined with muffin liners.

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.

Overhead shot of flour and sugar in a large mixing bowl.

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

An overhead shot of a mixing bowl with carrots apples raisins coconuts pecans added to flour.

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.

Overhead shot of a mixing bowl with a 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

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

A small tray of apple carrot muffins before going into the oven.

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!

Overhead shot of baked healthy apple muffins in a muffin tin.

💭 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

Are carrot cake muffins healthy?

How healthy your carrot cake muffins are depends on the recipe that you use. Some traditional carrot muffin recipes can contain copious amounts of processed sugar and butter or oil, increasing the calorie count and fat in the recipe. This carrot muffin recipe is pretty healthy, however, as it is made without any refined sugar and uses coconut oil instead of butter. Furthermore, these muffins are chockful of shredded apples, carrots, and raisins, adding both nutrition and flavor!

What is the secret to moist muffins?

The secret to moist muffins is to use sufficient fat and liquids, to not overmix the batter, and to whisk the wet ingredients and dry ingredients together separately before combining. This recipe contains coconut oil and juicy carrots and apples adding mouthwatering moisture to the final product. So, just follow the recipe steps, whisk the ingredients together separately, and don’t overmix the muffin batter before scooping into the muffin pan for moist and delicious muffins.

Healthy apple carrot muffins on the counter with shredded coconut and a jar of milk in the background.

🧇 More Healthy Breakfast Recipes!

Want to Save This Recipe?

Enter your email & I’ll send it to your inbox. Plus, get great new recipes from me every week!

Save Recipe

By submitting this form, you consent to receive emails from The Picky Eater.

Love this plant based breakfast recipe? Please leave a 5-star rating 🌟 in the recipe below and/or a review in the comments section further down the page!

You can also FOLLOW ME on FACEBOOK, TWITTER, INSTAGRAM, and PINTEREST to see more delicious, healthy, family-friendly food, and if you have any questions, I’m here to help!

📋 Recipe Card

🎥 Watch How to Make It

https://youtu.be/Y4PqGRxfpYw
Overhead shot of a small wire rack of healthy apple muffins with raisins, coconut, and a dish towel.
Print Recipe
5 from 20 votes

Healthy Apple Carrot Muffins

These healthy apple carrot muffins are low calorie and are one of our favorite muffin recipes for a recipe! These 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.
Prep Time15 minutes
Cook Time20 minutes
Total Time35 minutes
Course: Baking, Breakfast, Brunch, Snack
Cuisine: American
Diet: Vegetarian
Servings: 20 muffins
Calories: 230kcal
Author: Anjali Shah

Ingredients

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. Add applesauce and stir.
  • Spoon batter into muffin tins, filling at least ¾ full. Bake for 18 to 20 minutes or until golden. Serve warm.

Notes

Storage Directions
  • Storing: Store the 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.
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!
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

41 responses to “Healthy Apple Carrot Muffins”

  1. A neighbor shared a batch of these delicious muffins with us last week. They are fabulous! I asked her for the recipe, and here I am, excited to have it!5 stars

  2. This is such a delicious healthy version of apple muffins! Usually muffins are so high in sugar and fat that they’re more of a dessert than a breakfast option, but these are delicious and good for you!5 stars

  3. These breakfast muffins were so delicious. My son and I made them together and he is already asking if he can make them again soon!5 stars

    • Hi Marsha! I think bananas instead of sugar would work great! You could also just leave out the sugar altogether and not replace it with anything 🙂 I’ve done that before and it’s still very slightly sweet from the other ingredients and still tastes good!

    • Absolutely! I have just updated the printable version of the recipe with all of the nutritional information. Essentially, depending on which muffin tin you decide to use, you can end up with 20 large muffins or 30 mini muffins. Nutritional Information for 20 large muffins (per muffin): 230 calories, 14g fat, 197mg sodium, 25.3g carbs, 3.7g fiber, 11g sugar, 3.2g protein; 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. Hope this helps!

  4. These muffins were so delicious! Exactly what I had been looking for in a healthy muffin, yet never found! Will definitely be making these again…..and again! Thanks Anjali!5 stars

  5. Great chart – and good work with the muffins! I often try to make my baked goods more healthy too. The amount of oil and sugar in the original recipe is crazy!

    • Haha I completely agree – I’ve always thought that muffins are misleading, because even though they look like a healthy option, they’re so packed with butter and sugar they’re practically a cake! I hope you like this recipe when you try it, it’s definitely much much healthier than the original! 🙂

  6. Love the new site design! The healthy substitutions are great. Don’t forget the cashew cream as a great substitute for heavy cream! 🙂 Sometimes I will also substitue ground flax seed for a small portion of my flour. Your breakfast muffins look delish! I will definitely be trying these!5 stars

    • Yay thanks Lindsey! Omg you are totally right – cashew cream is absolutely amazing – it’s great in soups as a sub for heavy cream (and it keeps things vegan which is great!) I put ground flax seed on everything – it’s so good for you and is almost tasteless, so it’s perfect! Using it as a sub for flour is a great idea 🙂 Thanks for the tips!

  7. LOVE this post! I was just browsing the web for a healthy muffin recipe to use a a yogurt topping in the morning, so you answered my calling! Also love the substitutes. I love baking and being able to make it healthier without anyone noticing, so thank you!5 stars

    • Thanks so much Emily!! I’m so glad this is helpful for you! I can’t wait to hear what you think about the muffins! 🙂

  8. What a fun list! I love that many of the substitutions you suggest are also a better source of fiber. That’s awesome! And your new site design looks great! I love it!

    • That’s a great point! Not only are they lower in calories, but they’re also higher in fiber and nutrients! So glad you like the site design too!

      • So true! And with only 1 in 10 Americans getting enough fiber on a regular basis, it’s so important to offer fiber-rich options. Again, I love it!

      • Thanks Kati! (btw – I had no idea the ratio was that low, crazy!)

  9. I LOVE your new blog design! It’s beautiful!

    And thanks or the substitution ideas. I love subbing applesauce for oil. If you do it correctly, no one can ever tell the difference!5 stars

    • Thank you so much Parita!! 🙂 Totally agree with you about the applesauce – it’s one of my favorite secret healthy swaps!

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating




Subscribe to newsletter

Copyright 2024 The Picky Eater®, LLC. All rights reserved.