Healthy Carrot Muffins

Published by:
Liz Marino
| 04/06/2022 | Last Updated: 05/22/2025

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Healthy Carrot Muffins are the perfect gluten free treat! Packed with veggies + sweetened only with honey/fruit. They’re moist + delicious! This post is sponsored by my friends at Bob’s Red Mill.

A white plate filled with healthy carrot muffins

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Healthy Carrot Muffins are the perfect light and sweet treat. Sweetened with only honey and fruit and packed with veggies – they’re the perfect texture and taste amazing!

They almost tasted like carrot cake, but aren’t as sweet. (If you want a healthier cake recipe, try this Healthy Carrot Cake!)

What makes these Carrot Muffins healthy?

These muffins are actually good for you! Unlike many muffins loaded with sugar and fat – these are delicious and wholesome!

  • Heart healthy oils – I subbed the oil for a little less coconut oil, which is more nutritious than vegetable oil.
  • Sweetened with honey and fruit – the original recipe had white sugar, which I swapped with honey.
  • Veggies – It’s got carrots in it so it’s gotta be healthy, right?!
  • Gluten Free Oat Flour – I swapped white flour for Bob’s Red Mill Gluten-Free Oat Flour. This is one of my favorite gluten free flours to bake with. I find that it easily swaps into pretty much any recipe, and amps up the fiber/protein content.
Healthy carrot muffins on a white plate with a grey background and carrots on the side

Ingredients for Healthy Carrot Muffins:

Ingredients to make healthy carrot muffins in white bowls: shredded carrots, crushed pineapple, eggs, honey, coconut oil, gluten free oat flour, baking powder, baking soda, salt, cinnamon, and ground ginger.

We love these silicone muffin liners for baking!

How to make Healthy Carrot Muffins:

All wet ingredients for pineapple carrot muffins mixed together in a white bowl
  1. Mix your wet ingredients  (oil, eggs, and honey). Once those are combined, stir in your grated carrots and crushed pineapple.
Batter for pineapple carrot muffins mixed together in a white bowl
  1. Add in your spices, baking powder/soda + flour. The batter should be nice and thick!
healthy carrot muffin batter in muffin liners in a metal muffin pan uncooked
  1. Add the batter to a lined muffin tin + bake. 
Healthy Carrot Cake Muffins in a metal muffin pan fresh out of the oven
  1. In under 30 minutes, you’ll have perfectly cooked Healthy Carrot Muffins!
A close up of a healthy carrot muffin in a muffin tin.

Substitutions

These muffins are pretty versatile. Here are some substitutions for you!

Eggs: I haven’t tried making these muffins with an egg substitute so I’m not sure if it will work.

Honey: You can sub honey with maple syrup. I wouldn’t recommend coconut sugar.

Oil: You can use olive oil, avocado oil, vegetable oil, or melted butter in place of coconut oil.

Carrots: Grated carrots are not the same as pre-shredded carrots. We recommend grating whole carrots with a cheese grater!

Pineapple: I haven’t tried making this with fresh pineapple – but I think this would also work as long as you chopped it in VERY fine pieces. For canned pineapple – make sure it is unsweetened and just 100% pure pineapple! Make sure to drain it.

Canned Pineapple: If you don’t have crushed canned pineapple, you could sub applesauce or even mashed bananas, but we don’t recommend it.

Flour: I haven’t tried making these with any other flour, but I think it would work with gluten free 1:1 flour, or possibly with regular all purpose flour. If you try it, let me know!

To make vegan: I have not tried making these vegan. You might be able to sub eggs with flax eggs + add an extra 1/2 tsp baking powder but I do not know if it will work. Try flax eggs at your own risk! Sub honey for maple syrup.

Bread: I haven’t tried making this as a bread or cake but I think it might work. I think with the amount of batter you might only be able to get an 8×8 cake but I really am not sure. If you try it please let me know!

Mini Muffins: These work great as mini-muffins. They’ll need a little less time in the oven – probably around 10-12 minutes total to bake!

Raisins: A 1/2 cup of raisins would be a great addition to this and would make these muffins taste like carrot cake!

Cupcakes: You could turn these muffins into cupcakes, or try these Gluten-Free Carrot Cake Cupcakes.

A close up of healthy carrot muffins on a white plate

These healthy carrot cake muffins are so delicious that I honestly think you could put Healthier Cream Cheese Frosting on them and call them a cupcake. They could totally pass off as carrot cake’s less sweet/heavy cousin, but no matter how you make them I think you’ll love them!

I’m definitely going to be bringing these to my Easter brunch to share with family- you should too!

Storage

Storing Carrot Muffins: You can store these muffins covered on your counter for a few days, but I recommend keeping them in the refrigerator for freshness! The muffin will last up to a week in the refrigerator – but will lose their freshness after about 3 days on the counter.

Freezing: I like to freeze muffins in a reusable Ziploc bag or an air-tight container. It’s best not to stack them on one another when freezing because they may stick together. When you’re ready to serve – pop in the microwave or the toaster oven until they’re warmed through.

A hand holding a healthy carrot muffin over a plate of carrot cake muffins
A white plate filled with healthy carrot muffins

Healthy Carrot Muffins

Recipe by: Liz Marino
4.85 from 20 votes
Healthy Carrot Muffins are the perfect gluten free treat! Packed with veggies + sweetened only with honey/fruit. They’re moist + delicious!
Prep Time : 5 minutes
Cook Time : 25 minutes
Total Time : 30 minutes
Serves : 12 muffins
(hover over # to adjust)

Ingredients

Instructions

  1. Preheat oven to 400 and prepare a greased or lined muffin tin. (We like silicone muffin liners)
  2. In a bowl, whisk together eggs, honey and melted coconut oil until smooth. Stir in grated carrots + pineapple. 
  3. Add in oat flour, baking powder, baking soda + spices. Stir until combined. Batter will be slightly thick. 
  4. Pour 1/3 cup of batter into greased muffin tin. They should be filled to the top of the liner but not overflowing.
  5. Bake the muffins for 20-25 minutes until muffins are golden brown + toothpick comes out clean when inserted into the center.

Video

Nutrition Facts

Serving: 1muffin | Calories: 255kcal | Carbohydrates: 34g | Protein: 5g | Fat: 12g | Saturated Fat: 9g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 41mg | Sodium: 218mg | Potassium: 224mg | Fiber: 3g | Sugar: 20g | Vitamin A: 3647IU | Vitamin C: 6mg | Calcium: 33mg | Iron: 1mg
Course: Breakfast
Cuisine: American
Tried this recipe?Share it! Make sure to tag @thecleaneatingcouple or use #thecleaneatingcouple!

4.85 from 20 votes (6 ratings without comment)

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Recipe Rating




33 Comments

  1. 5 stars
    absolutely amazing. !!

  2. Keli M Drew says:

    5 stars
    This recipe was so easy to throw together while i was cooking dinner and we had fresh warm delicious cartot pineapple muffins for dessert. I highly recommend giving it a try.

  3. 5 stars
    i added salt ~3/4 tsp based on typical recipes and the comment about the muffins tasting bland. i don’t have to be on a low-sodium diet, and i like how it brightens up the flavor of food in general. they look gorgeous and smell great so i can’t wait for them to cool……..hmmmmm, after 25+mins they’re a little undercooked but the flavor is nice!

    1. The Clean Eating Couple says:

      I definitely would not add that much salt and I’m not sure what you are referring to with people calling these bland. Glad you liked them though!

  4. 5 stars
    Loved these! So moist with a hint of sweet- and the spice mixture is on point!
    Made a few subs:
    -used regular white flour
    -instead of canned pineapple I used 15oz can pears drained and one ripe banana

    Delicious!!

  5. 5 stars
    Did these the other day. So delicious

  6. MARY E YEAGER says:

    2 stars
    I followed the recipe exactly and have to say the muffins are pretty tasteless. The consistency of them is fine and they look just as portrayed in the recipe but they don’t taste good. Very disappointed as I have always had great luck with your recipes!

    1. The Clean Eating Couple says:

      Hi Mary – I’m really sorry to hear this. Did you change any ingredients? These muffins should taste like carrot cake. If you made ingredient substitutions it could result in a different muffin. Especially if you cut down the sugar.

  7. 5 stars
    Excellent. I also added walnuts and raisins. Absolutely, super moist and very tasty. They are much better tasting using the oat flour. I found this recipe easy to follow and I will be making them again! Thank you for sharing this healthy version.

  8. I’m sure these are incredibly delicious and they use clean ingredients but at 20 g of sugar and 250 calories I do not think I could hand that to my child

    1. The Clean Eating Couple says:

      If you don’t want to make them for your family, no one is forcing you to! The sugar comes from crushed pineapple, carrots, and honey. These muffins are made with all whole food ingredients. A far better option than white sugar, white flour, or vegetable oil which most carrot muffins are made from.

  9. 5 stars
    I just made these and they turned out really really good – thank you! I ground up oats in blender to make oat flour as I did not have any. The muffins turned out nice and moist and sweet from honey – thank you again!

    1. The Clean Eating Couple says:

      So glad you liked them!

  10. 5 stars
    These muffins are fantastic! I love baked goods but I don’t like using sugar and it was nice to find a gluten free healthy muffin without sugar. My family has a ton of eating restrictions and this is the only food blog I have found that has recipes that are clean enough for most of them to eat!

    1. The Clean Eating Couple says:

      Thank you so much Grace!! I’m so glad you love the recipes -that makes me so happy to hear!

      1. I have only canned sliced pineapple . Will it work if I chop it finely?

        1. I haven’t tried it so I can’t be sure – sorry! I think it would probabaly work as long as they’re chopped really finely!

  11. 5 stars
    Made these with my six year old today. Love that there’s no sugar in them. I also snuck some ground flaxseed in the mix. Thanks for sharing!

    1. The Clean Eating Couple says:

      So glad you liked them, Marty!!

  12. lois chaput says:

    could this be made into a 9by 13 in cake?

    1. The Clean Eating Couple says:

      Hi Lois – I haven’t tried this but I think it might work. I think with the amount of batter you might only be able to get an 8×8 cake but I really am not sure. If you try it please let me know!

  13. 5 stars
    Made these and they were very good. Used regular flour because that was all I had on hand. Carrots were from our garden, eggs from our chickens, and honey from our bees. Topped them with homemade cream cheese frosting. Yum!

    1. The Clean Eating Couple says:

      So glad you liked them, Tammy! The cream cheese frosting sounds delicious!

  14. 5 stars
    Love these! I make these without the oil and substitute half the pineapple for one grated zucchini and they turn out so sweet and moist!! Perfect midday snack or to sneak an extra serve of veg in for the kiddies (or hubbies!)

    1. The Clean Eating Couple says:

      I love that idea of sneaking in the veggies!! Totally going to try that – Thanks Jessica!

  15. 5 stars
    Great recipe! Mine came out a little more grainy than fluffy- I used flax egg and made my own oat flour so that could be why. Nonetheless I still loved them and my mom and sister did as well! Great flavor and perfect breakfast/ snack for the summer! Thank you!

    1. The Clean Eating Couple says:

      Thank you so much, Tara! I’m so glad you liked them – this makes me so happy to hear. Glad the modifications came out great 🙂

  16. Wendy Martineau says:

    5 stars
    These have quickly become my favorite breakfast muffin! They are super easy to make and they keep well all week (we meal prep on Sunday). The carrots make me feel like I am eating healthy and getting my veggies. The pineapple keeps them really moist without making they too sweet. It’s the perfect flavor combination. I have some already made up right now, and can’t wait until breakfast tomorrow!

    1. The Clean Eating Couple says:

      I’m so glad you like them Wendy!! They’re one of my favorite breakfasts too. So yummy!! They freeze really well (if you have any that last that long!!)

  17. I’ll try this recipe for the weekend, and fingers crossed it will go well!

    1. The Clean Eating Couple says:

      I think you’ll love it, Jo!

  18. Do you drain the juice from the pineapple?

    1. The Clean Eating Couple says:

      Yes you do! I’ve updated the recipe to make it a little clearer 🙂