Healthy Apple Carrot Muffins
This post may contain affiliate links. As an Amazon Associate, I earn from qualifying purchases. Please read my disclosure.When I’m craving a snack that’s both nutritious and satisfying, I always turn to my Healthy Apple Carrot Muffins. Made with fresh apples, carrots, cinnamon, unsweetened applesauce, and coconut sugar, they’re naturally sweet and packed with fiber. Whether it’s a quick breakfast, a nutritious treat for my family, or a mid-afternoon pick-me-up, these muffins never disappoint.
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As a mom, I’m always on the lookout for snacks that are both wholesome and kid-approved. My little ones love muffins, but I wanted something that wasn’t packed with refined sugar. That’s what inspired me to create these healthy apple carrot muffins, they are so moist and fluffy much like my vegan chocolate chip muffins.
From the very first batch, I was hooked! These, also called “superhero” muffins are ridiculously easy to make, perfect for stashing in the freezer for busy mornings, and, best of all, my family loves them.
👩🏽🍳 Why I Love This Recipe
How could I not love the amazing smell of these muffins, made with two of my all-time favorite ingredients? It’s just not possible!! And it’s not just me, my husband and kids are obsessed with them too. So in our house, skipping a batch or not loving these muffins? Yeah, not an option! Ha!
What I love most about these, also known as sunshine muffins (besides how insanely good they taste) is how flexible they are! I can easily make them gluten-free or vegan with a few simple swaps, and since they’re naturally sweetened with apples, carrots, and a touch of coconut sugar, there’s no refined sugar in them. That means I can toss them into lunchboxes, pack them for road trips, or grab one for myself when I need a quick energy boost, because let’s be honest, moms need snacks too!.
Every bite reminds me of my vegan carrot cake, soft, perfectly spiced, and with just the right amount of crunch. And let’s be real, when a recipe is this good and kid-approved, you know it’s a keeper! Simple ingredients, easy steps, and a muffin that brings joy to everyone, what’s not to love?
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🥘 Ingredients
I always keep these staple ingredients on hand to make my apple carrot muffins recipe.

Flour & Baking Soda: I use a mix of all-purpose flour and white whole wheat flour for a perfect balance of softness and whole grain goodness. Baking soda helps the muffins rise, making them light and fluffy.
Warm Spices: Cinnamon brings that cozy, spiced flavor that pairs perfectly with apples and carrots. A touch of sea salt enhances all the flavors, making every bite even more delicious.
Natural Sweeteners: Instead of refined sugar, I use coconut sugar for its warm, molasses-like notes.
Fruits & Veggies: Freshly grated carrots and apples add natural sweetness, fiber, and moisture. Raisins add a little chewy sweetness, and shredded coconut gives a subtle nuttiness, and chopped pecans give the perfect crunch and a boost of healthy fats.
Healthy Fats & Binders: Eggs hold everything together and help create a great texture (room temperature eggs work best!). I use melted coconut oil for moisture.
Extra Moisture & Depth of Flavor: Unsweetened applesauce adds even more natural sweetness and keeps the muffins extra soft. A splash of pure vanilla extract rounds out the flavors for the perfect muffin!
🍲 Substitutions
Flour: oat flour works as a perfect 1:1 swap for gluten-free option.
Apples: I love using Granny Smith, Fuji, or Pink Lady apples, but any fresh apple will work.
Nuts: No pecans? No problem! Walnuts or slivered almonds make great substitutes.
Extract: If I’m out of vanilla, almond extract works just as well and adds a slightly nutty twist.
Applesauce: Mashed bananas or pureed pears are great swaps for applesauce and add their own natural sweetness.
🔪 How To Make
This apple carrot muffins recipe is as easy as it gets, and I love how quickly they come together.
Prepare The Muffin Tin: I start by preheating my oven to 375°F and lining a muffin tin with baking cups. If I’m not using liners, I simply spray the muffin tin with non-stick cooking spray.
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Sift Dry Ingredients: In a large mixing bowl, I sift together the all-purpose flour, whole wheat flour, cinnamon, baking soda, and salt. Then, I stir in the coconut sugar until evenly mixed.
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Stir In Apples, Carrots, And Raisins: This is where all the natural sweetness and texture come in! I gently stir in the shredded carrots, grated apples, raisins, coconut, and chopped pecans until everything is evenly distributed.
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Combine Wet Ingredients: I whisk the eggs in a small or medium bowl, then add the oil and vanilla extract, whisking everything together until smooth. Next, I make a well in the dry ingredients and pour in the egg mixture, ready to bring the batter to life!
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Combine Wet And Dry Ingredients: I gently mix the eggs into the batter until just combined, making sure not to overmix. Overmixing can lead to tough muffins, and we definitely want them soft and fluffy!
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Transfer Batter To Pan: I spoon the batter into the prepared muffin cups, making sure each one gets an equal amount.
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Bake: I pop the muffin tin into the preheated oven and bake for 18-20 minutes, until they turn a beautiful golden brown. Once done, I transfer them to a wire rack to cool before digging in, though I can never resist sneaking one while they’re still warm.
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💭 Expert Tips
My #1 Secret Tip for keeping my healthy apple carrot muffins soft and fluffy is to mix the batter as little as possible! I used to think more mixing meant better muffins, but I quickly learned that overmixing leads to dense, tough bites, not what I want! Now, I gently fold everything together just until combined, even if there are a few lumps. It feels a little too easy, but trust me, this simple trick makes all the difference for light, tender muffins every time.
Other Tips To Keep In Mind:
- Make Mini Muffins: I use a mini muffin pan and scoop 2-3 tablespoons of batter into each cup. They bake in just 11-13 minutes, turning into perfectly bite-sized treats.
- Muffin Liner Options: Paper or silicone liners make cleanup easy, but if I don’t have any, a quick spray of non-stick cooking spray does the trick. No sticking, no mess.
- Maple Syrup Adjustments: If I swap coconut sugar for maple syrup, I mix it in with the wet ingredients. This helps it blend smoothly into the batter for even sweetness.
📖 Variations
One of the best things about these healthy apple carrot muffins? You can mix things up and make them your own.
Protein Muffins: I whisk in 2-3 tablespoons of peanut or almond butter with the wet ingredients for an extra boost of protein and fiber. A scoop of protein powder mixed into the dry ingredients works great too.
Blueberry Muffins: I swap out the raisins for an equal amount of dried blueberries. It’s a fun twist that adds a little burst of fruity flavor.
Seasonal: I add ½ cup of pumpkin puree and reduce the applesauce by the same amount for a cozy fall-inspired twist. A little pumpkin pie spice instead of some of the cinnamon takes the flavor to the next level.
Banana Flavor: I mix in ½ cup of mashed ripe banana and cut back the applesauce by ½ cup. For an even stronger banana flavor, I swap all the applesauce for banana puree and sometimes switch out the pecans for walnuts.
🍽 Serving Suggestions
These healthy apple carrot muffins are delicious on their own, but I love pairing them with other wholesome foods to make a balanced meal or snack.
Breakfast Boost: I serve them with a side of Greek yogurt and a drizzle of my vegan honey or my vegan Nutella for extra protein and creaminess.
On-the-Go Snack: A muffin with a handful of nuts or fresh fruit makes the perfect grab-and-go energy boost.
Brunch Favorite: These muffins pair beautifully with my refreshing pineapple and banana smoothie, or a hot cup of coffee for a satisfying start to the day.
🫙 Storage Directions
Refrigerating: I keep these muffins in an airtight container at room temperature for 2-3 days, or if I want them to last longer, I pop them in the fridge for up to a week.
Freezing: When I make a big batch, I freeze them in a freezer-safe bag for up to 6 months. When I’m ready to enjoy one, I just let it defrost at room temperature for 20-30 minutes or warm it up for a few seconds in the microwave for that fresh-baked taste.
❓Recipe FAQs
I make sure not to overmix the batter! I stir just until everything is combined, some lumps are totally fine. Overmixing can make the muffins dense and tough, and I want them soft and fluffy every time!
The secret to moist muffins is all about balance! I make sure to use enough fat and liquids, avoid overmixing, and always whisk the wet and dry ingredients separately before combining. This recipe has coconut oil, juicy carrots, and apples, which add amazing moisture, so as long as I follow the steps, mix gently, and scoop the batter straight into the muffin pan, I know I’ll get perfectly soft and delicious muffins every time!
It’s super easy to make these muffins vegan! I just swap the eggs for flax eggs (1 tablespoon flaxseed meal + 3 tablespoons water per egg) and use maple syrup instead of honey if needed.
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🎥 Watch How to Make It
Healthy Apple Carrot Muffins
Ingredients
- 1 cup all-purpose flour
- 1 cup white whole wheat flour or whole wheat pastry flour
- 2 tsp ground cinnamon
- 2 tsp baking soda
- ½ tsp salt
- ½ cup coconut sugar or pure maple syrup
- 1½ 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 tsp 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. 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
- My #1 Secret Tip for keeping my healthy apple carrot muffins soft and fluffy is to mix the batter as little as possible! I used to think more mixing meant better muffins, but I quickly learned that overmixing leads to dense, tough bites, not what I want! Now, I gently fold everything together just until combined, even if there are a few lumps. It feels a little too easy, but trust me, this simple trick makes all the difference for light, tender muffins every time.
- I use a mini muffin pan and scoop 2-3 tablespoons of batter into each cup. They bake in just 11-13 minutes, turning into perfectly bite-sized treats.
- Paper or silicone liners make cleanup easy, but if I don’t have any, a quick spray of non-stick cooking spray does the trick. No sticking, no mess.
- If I swap coconut sugar for maple syrup, I mix it in with the wet ingredients. This helps it blend smoothly into the batter for even sweetness.
I will be making these muffins again! They’re so tasty. Thank you for a great recipe, Anjali!
Yay! Thanks Kristine!
These muffins look amazingly delicious. Perfect fall treat. I wish I could grab one right away.
Thank you so much! I’m sure you will love this recipe!
These look absolutely fantastic. Thank you for all of the in depth directions!
Thanks Blair! I hope you love these as much as we do!
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!
Oh awesome!! That’s so wonderful to hear Denay!
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!
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!
Aw yay!! I’m so happy to hear that Emily!
Could you add or substitute blueberries for the sugar in this? How about bananas instead of sugar?
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!
Can you post the nutrition facts so I can figure out weight watcher points?
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!
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!
Yay!! That’s so awesome – I’m so happy to hear that Annabelle! 🙂
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! 🙂
What a fabulous recipe, these look absolutely delicious!! 🙂
Thanks so much Kelly!! I’m sure you will love them!
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!
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!
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!
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! 🙂
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!)
Anjali! Thank you for this! It’s wonderful! 🙂 xo R
No problem at all! So glad you like it Rosie!
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!
Thank you so much Parita!! 🙂 Totally agree with you about the applesauce – it’s one of my favorite secret healthy swaps!