Healthy Carrot Pumpkin Muffins with Cream Cheese Frosting

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These Healthy Carrot Pumpkin Muffins with Cream Cheese Frosting may or may not be one of my favorite recipes to date. Bold statement, I know, but Y U M.

healthy carrot pumpkin muffins with cream cheese frosting

Hey, Hi, Hello, How Are you?

Apologies for my hiatus. I’ve been very busy lately and haven’t had a chance to post any recipes or blog posts in general. I hope you have been enjoying your February so far, despite the ridiculous winter weather we’ve been having.

If you’re not in Kansas City, have you been getting absolutely DUMPED on with snow, too?! Ugh. Forever dreaming of sunshine and warmth. That damn groundhog lied. What’s new.

Anyway, I have some really exciting things in the works for my blog, and I can’t wait to share more about that very soon. Stay tuned. : )

Like I said, it’s been a hot second since I posted a recipe, but trust me when I say this one is going to be worth the wait. If you know me well, you know that I absolutely love carrot cake, and I absolutely love all things pumpkin.

I have been thinking up a carrot cake-like recipe for a while, and it finally came to fruition a few weekends ago when I actually had some time to bake.

Inspiration behind these healthy carrot pumpkin muffins

This recipe was inspired by a few different recipes I came across on Pinterest, including my own Healthy Gingerbread Muffins, and it is pretty damn delicious if I do say so myself.

I confessed to my followers on Instagram that I made a huge baking mistake on my first go-round with this recipe, and I am fully putting the blame on coconut oil. I have had issues with coconut oil the past several times I have baked something that called for it.

healthy carrot pumpkin muffins with cream cheese frosting

Because it is solid, and usually has to be melted, I stick it in the microwave and forget it is in there until the baked good has already been placed in the oven. This time I remembered to take it out of the microwave, and yet, it still didn’t make its way into the batter. It just blended right into the dish and hung out on the counter while my muffins baked away.

Can we form a petition to make coconut oil brightly colored instead of clear so this stops happening to me? LOL. But seriously…

healthy carrot pumpkin muffins with cream cheese frosting

Nonetheless, my muffins turned out great the first time, but I knew the coconut oil would’ve added the perfect amount of sweetness to take them to the next level. These are super dense, tasty and packed with nutrition.

what’s a carrot-flavored dessert without cream cheese frosting?

Since I am such a carrot cake lover, I felt the urge to create some kind of healthier cream cheese frosting, because honestly, what is carrot cake without cream cheese frosting?!

Of course, you can omit the frosting if you want, but I highly recommend adding it. Totally your call. Does frosting make them cupcakes? Asking for a friend…

healthy carrot pumpkin muffins with cream cheese frosting

Either way, I also recommend adding white chocolate chips because the carrot + pumpkin + white chocolate combo is SO BOMB.

I’m happy to report that coconut oil made it into the recipe for round two, and they are even more delicious than I imagined. Here’s the recipe!

healthy carrot pumpkin muffins with cream cheese frosting

Healthy Carrot Pumpkin Muffins with Cream Cheese Frosting

Shanna Hutcheson
These muffins are loaded with vitamins, minerals and fiber thanks to the pumpkin puree, carrots and whole wheat flour, plus tons of other goodies! The cream cheese "frosting" is the cherry on top, and it's healthy enough that you can still get away with eating these babies for breakfast. Muffins or cupcakes? YOU decide. 😉
4.91 from 10 votes
Prep Time 15 minutes
Cook Time 15 minutes
Total Time 30 minutes
Course Breakfast, Dessert
Cuisine American
Servings 18 muffins
Calories 160 kcal


  • 2 cups whole wheat flour
  • 1 Tbsp baking powder
  • 1 tsp baking soda
  • 2 tsp ground cinnamon
  • 1/2 tsp ground ginger
  • 1/4 tsp ground nutmeg
  • Pinch of salt ~1/8 tsp
  • 2 eggs
  • 1 cup pumpkin puree
  • 1/2 cup plain Greek yogurt
  • 1/2 cup unsweetened applesauce
  • 1/4 cup maple syrup
  • 1/4 cup unsweetened vanilla almond milk
  • 3 Tbsp coconut oil melted and cooled
  • 1 cup finely shredded carrots 2-3 large carrots, shredded in food processor
  • 1 tsp vanilla extract

Optional Mix-Ins:

  • 1/3 cup chopped walnuts
  • 1/3 cup white chocolate chips

Cream Cheese Frosting

  • 1/2 cup plain whipped cream cheese
  • 1/2 cup plain Greek yogurt
  • 1/2 tsp cinnamon
  • 1/2 tsp vanilla extract
  • 2 tsp honey


  • Preheat oven at 350° F. Grease two muffin pans with non-stick cooking spray. (Mine made 18 muffins)
  • Peel large carrots and chop into 2 inch chunks. Place in food processor and pulse until finely shredded. Repeat until you have 1 cup of shredded carrot. I used 2-3 large carrots.
  • In a large bowl, combine dry ingredients: whole wheat flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Set aside.
  • In a medium bowl, beat 2 eggs. Add Greek yogurt, maple syrup, coconut oil, pumpkin puree, unsweetened applesauce, unsweetened vanilla almond milk, vanilla extract, and shredded carrots. Mix well.
  • Pour wet ingredients into dry ingredients. Add additional mix-ins as desired, including chopped walnuts and white chocolate chips. Stir until just combined. Do not over-mix. Pour batter evenly into prepared muffin cups.
  • Bake for 13-15 muffins, or until a knife inserted in the center comes out clean.
  • While muffins are baking, prepare cream cheese frosting by combining cream cheese, Greek yogurt, cinnamon, vanilla and honey in a small bowl. Mix well. Let muffins cool for 15-20 minutes before adding frosting.
  • Store in the refrigerator for 3-5 days in an airtight container, or transfer to the freezer in freezer-safe bags. Reheat in the microwave to thaw. If not adding frosting, serve with a dollop of almond butter on top, if desired.


Calories: 160kcalCarbohydrates: 19gProtein: 4gFat: 7gSaturated Fat: 4gCholesterol: 26mgSodium: 115mgPotassium: 231mgFiber: 2gSugar: 7gVitamin A: 3415IUVitamin C: 1.1mgCalcium: 82mgIron: 1mg
Keyword carrot cake, cream cheese frosting, cupcakes, healthy breakfast, healthy carrot pumpkin muffins, healthy recipe, meal prep, muffins
Tried this recipe?Let us know how it was!
healthy carrot pumpkin muffins with cream cheese frosting

That’s all, folks! I hope you love these Healthy Carrot Pumpkin Muffins with Cream Cheese Frosting as much as we do!

As always, please tag me in your creations at @wellnessforthewin on Instagram or my Facebook page, and pin this on Pinterest so you can make it over and over again! I can’t wait to hear what you think!



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    1. I think that should be fine! I haven’t tried that so I can’t say what the flavor will be like, but consistency-wise I don’t think it’ll make a difference. Let me know how it goes! 🙂

  1. 4 stars
    Hey there! Just made these for the first time. I don’t have all the ingredients for the icing, so I just did a little cinnamon sugar topping which was nice & needed I think – the muffins aren’t super sweet (which I normally like!) but I think the topping definitely adds some more flavor/sweetness! 6 of the muffins I added raisins which also added some good flavor.

    I am not a baking expert by ANY means! But the reason I’m giving the recipe 4/5 stars is probably mostly because there’s a lot of ingredients – applesauce, pumpkin, yogurt, milk and oil – would it be possible to simplify this? I know often times these are used for moisture, so I thought it seemed a little redundant. But again, I am NO EXPERT – and the texture of the muffins was DELISH! Very moist.

    Next time, I’ll probably add some more maple syrup or maybe just use regular sugar, plus some more of the spices – considering if I’m not making the frosting topping. Thanks for the recipe, Shanna! 🙂

    1. Hi Lauren – thank you so much for your review and honest feedback; I really appreciate it! Love the idea for a cinnamon sugar topping. 🙂 Yes, the muffins are not meant to be overly sweet so they can be a good, healthy breakfast option. But definitely feel free to add as much sweetness as you’d like! I understand what you’re saying about the amount of ingredients and maybe I’ll do some testing to see if I can reduce or simplify, although I like the unique components that each one has to offer. 🙂 And as always, feel free to use regular sugar or whatever you need! That’s the beauty of cooking; you can always personalize to suit your tastes! Thank you again for the review. Take care! – Shanna

  2. 5 stars
    I love these muffins! I had all the ingredients on hand and found the recipe easy to follow. I froze half the batch (which I thanked myself for when I remembered them). I loved the icing but also loved them with almond butter. Highly recommend making these!

    1. Aw, thank you so much! So glad to hear that you love them, and glad you found it easy to follow. It does have quite a few ingredients, but luckily they are pretty common ones that most people have! Yay! Appreciate your feedback!

  3. 5 stars
    These muffins are very good! Love how moist they are. Sweetness is just right for me. I subbed honey, regular milk, and canola oil as it’s what I had on hand. Didn’t do the icing this time but will add almond butter or whipped cream cheese on top.

    1. Yay! I’m so glad you liked them and those are all perfect substitutions! Way to be resourceful. 🙂 Thank you so much for your review! And they are delish with either of those on top!

  4. 5 stars
    My boyfriend and I LOVE these muffins! I made them several times last fall and shared the recipe with a few friends and family who also enjoyed them. I have tried the muffins with the frosting, white chocolate chips, and dark chocolate chips. My favorite is mini chocolate chips and no frosting with a little peanut butter or almond butter on top. But honestly they are delicious no matter what you put on them! I am looking forward to making them again this fall. Thanks Shanna for sharing such delicious and nutritious recipes 🙂

    1. Mmm, so many good variations! 🙂 Thank you so much for sharing with friends and family – that means a lot! Hope you enjoy them this fall, too! 🙂

    1. Aw, thank you Mallory! So happy you love them! That’s the perfect method so you don’t have to worry about them going bad. So glad you love the frosting, too; my favorite part. 😉

  5. 5 stars
    These muffins are amazing! Don’t be scared away by the carrots; you can’t taste them. The “frosting” is delicious and adds just the right a touch of sweetness. I’ll be making these on repeat this fall!

  6. 5 stars
    These are a really good and moist. I subbed the ginger and nutmeg for a 1/2 teaspoon of pumpkin pie spice that I had on hand. I love spice cakes and this hit all the right notes for me! Next time I’ll add some walnuts 🙂

    1. Yay! Pumpkin pie spice is a perfect substitute! 🙂 Definitely add walnuts next time — I love the added crunch! And any kind of chocolate chips are pretty yummy, too. ; )

  7. 5 stars
    just made these for the first time, so delish! Easy to make and love that they are a healthy option. I don’t feel guilty for eating more than one at a time! thanks for the recipe

  8. Hi, this recipe sounds delicious! My son has a severe egg allergy and when I bake I typically sub applesauce for egg. However, I see that applesauce is already an ingredient. Curious what ideas you had to sub for the egg for this recipe?

    Thank you!

    1. Hi Jaime! Thank you for reaching out! I would recommend using a “flax egg” for a substitute. If you Google “how to make a flax egg” lots of results will come up, but here is one you might try: — this will be helpful for you in future recipes too, I’m sure! 🙂 Let me know how it goes!

  9. 5 stars
    Such an easy recipe that I had all the ingredients on hand for! Since the muffins aren’t extremely sweet, they will make a perfect easy weekday breakfast. Love all of Shanna’s recipes that I’ve tried!

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