Carrot Butternut Whole Grain Muffins

These kid-friendly carrot butternut whole grain muffins are naturally sweetened and totally delicious!

These kid-friendly carrot butternut whole grain muffins are naturally sweetened and totally delicious!

Naturally sweetened with pure maple syrup, these whole grain muffins are filled with freshly grated carrots, pureed butternut squash, and contain a few healthy extras like almond meal and flax.

They’re perfect for tiny tummies and, though I made them with my wild and crazy toddler in mind, I love snacking on them too!

Yes, I said squash. Don’t give me that look! Remember how awesome zucchini tastes in baked goods? Butternut is equally fabulous and plays a similar role to applesauce by replacing a bit of the fat with buttery, flavorful produce!

The result is a fluffy muffin that is tender and moi— I won’t dare say it for fear you’ll go running from the room with your hands covering your eyes. Don’t do that; you’ll surely run into a wall. This is coming from a girl who has a rockin’ Harry Potter scar on her forehead for doing just that. Though I had a 4ft stuffed polar bear obstructing my vision, because… well I have no idea why but I’m sure they got a kick out of it in the ER!

Go big or go home, right?

These kid-friendly carrot butternut whole grain muffins are naturally sweetened and totally delicious!

Anywho! These are great way to sneak a boatload of beta carotene into your friends and family. If you’re feeding them to ankle biters, I suggest leaving them just barely sweetened as written in the recipe. Trying to trick adults? You may need a little extra sweet stuff to appease their sugar-lovin’ palate. Either that, or make them these yummy Carrot Coconut Muffins.

Though you guys know me, I looove savory breakfast breads and will happily slather some butter on pretty much anything and call it breakfast because in my world butter > sugar. Always. Unless you’re having a bad day. Then you need both.

Carrot Butternut Whole Grain Muffins

Carrot Butternut Whole Grain Muffins - kid-friendly and parent-approved! We LOVE these muffins!
5 from 7 votes

Carrot Butternut Whole Grain Muffins

These kid-friendly carrot butternut whole grain muffins are naturally sweetened and totally delicious!

Course Breakfast
Cuisine American
Keyword Butternut Whole Grain Muffins
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Servings 10 servings
Calories 148 kcal
Author Jenn Laughlin - Peas and Crayons


  • 1 cup whole wheat flour
  • 1/3 cup white whole wheat flour
  • 2 TBSP almond meal (ground almond)
  • 1 TBSP ground flax
  • 3/4 tsp baking soda
  • 3/4 tsp baking powder
  • 1/2 tsp cinnamon
  • 1/4 tsp salt
  • 2 large eggs
  • 1/2 cup milk (dairy, coconut, almond)
  • 1/4 cup pure maple syrup
  • 3 TBSP melted butter
  • 1 tsp vanilla
  • 1 cup freshly grated carrot
  • 1/4 cup pureed butternut squash


  1. Pre-heat oven to 350 degrees F.
  2. Line a muffin tin with paper baking cups or spritz with your favorite oil spray. I used the liners.
  3. In a medium bowl, combine flours with almond meal, flax, baking soda, baking powder, cinnamon, and salt and whisk to mix.
  4. In a large bowl, combine lightly beaten eggs with milk, maple syrup, melted butter, and vanilla. Whisk until incorporated.
  5. Next blot the excess moisture from your carrot and add to the egg bowl along with your pureed butternut squash.
  6. Slowly sift the flour mixture into the egg mixture, using a fork to mix.
  7. Once the mixture is just combined, pour into muffin cups.
  8. Lay muffin tin atop a baking sheet to prevent over-browning of the muffin bottoms. This is totally optional but a favorite trick of mine as of lately!
  9. Bake at 350F on the center rack for approximately 25 minutes, inserting a toothpick into the center to check for a fluffy, full-cooked interior.
  10. Allow to cool on a wire rack then dig in!

Recipe Notes

After making nearly a dozen batches of these muffins since they first entered my kitchen, I started using parchment paper muffin liners which are pretty much my new favorite thing ever! Hunt. These. Down. I use them for nearly all my muffins and cupcakes now! Hello easy cleanup and zero lost muffin crumbs!

This tasty recipe will absolutely work if you use all-purpose flour or if you need to skip the white whole wheat flour and use all 100% whole wheat flour instead. If you have any questions don't hesitate to ask - we make these muffins at least once a month and I make adjustments depending on what we have in the fridge/pantry at that time.

If you’re feeding them to kiddos like moi I suggest leaving them just barely sweetened as written in the recipe. Trying to trick adults? You may need a little extra sweet stuff to appease their sugar-lovin’ palate.

Nutrition Facts
Carrot Butternut Whole Grain Muffins
Amount Per Serving
Calories 148 Calories from Fat 54
% Daily Value*
Fat 6g9%
Saturated Fat 2g13%
Cholesterol 43mg14%
Sodium 211mg9%
Potassium 193mg6%
Carbohydrates 20g7%
Fiber 2g8%
Sugar 6g7%
Protein 4g8%
Vitamin A 2685IU54%
Vitamin C 1.5mg2%
Calcium 64mg6%
Iron 0.9mg5%
* Percent Daily Values are based on a 2000 calorie diet.

My little guinea pig gobbled them up! I froze half the batch for later and we’re already down to just one fresh muffin for breakfast tomorrow. A serving for her is about half a muffin and the fact that she’s still plowing through these means they’ll absolutely be made again!

Chickpea Approved Carrot Butternut Whole Grain Muffins

It comes as no surprise that the most commonly heard baby babble in this house is

Eat! Dis? Eat dis? Eat!

:: UPDATE :: over a year later + these are STILL her favorite muffins; she even helps me make them! I often double the batch so I can freeze some for busy days and on-the-go snacking. Simply reheat for about 30 seconds and you’re good to go!

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Recipe Rating


  • Kathy

    I’d like to try these, but I don’t have almonds, almond meal, or flax. Can I leave them out of the recipe? Or should I substitute in…something else?

  • 5 stars
    So good. I would give 5stars if my device would cooperate.
    This only thing that I did add was more cinnamon (1 tsp.) and 1 Tbsp. Orange zest.
    Thanks again

  • Megan Palacios

    Hello, I made this last night and put them in a zip lock bag and then in the fridge. This morning I took one out and saw it had green in it, as if I had used zucchini… which I did not. Has this happened with you? I have no clue what could turn green.

    • Hey Megan! I have no idea… I’ve never seen them turn green before! We always store ours individually wrapped in plastic on the counter for the first 1-2 days or so and then any leftovers get frozen to reheat later.

  • Jen

    5 stars
    What a delicious recipe! I made them this morning and…. mmmm. My toddler has had 2 already on top of his normal breakfast. I’m making several more batches to freeze and am adding chopped pecans and maybe one with some no-sugar-added raisins. Maybe I’ll play around with some other ingredients as I clear out the fridge, haha. It’s the perfect base recipe! Thank you, thank you!

    • Loooove the extras you’ve been adding – raisins and pecans sound amazing! Thanks for your sweet review, Jen!

  • Kathy

    Can I substitute something for the almond and ground flax?

    • Hi Kathy! I added those so the muffins would have extra fiber and nutrients but they’re for sure swappable when either ingredient isn’t around! I haven’t had a chance to test it to see if more moisture needs to be added (no one wants dry muffins!), but 2-3 TBSP of flour in place of both ingredients should be fine! Let me know if you get a chance to experiment! xo

  • Kathleen Parisotto

    5 stars
    I made these tonight but had to sub a few items. Didn’t have any maple syrup so used brown sugar. Subbed oil for butter, added some shredded coconut. Delish!!!!

  • Dani

    Hey Jenn! Have you tried using anything beside eggs? We are vegan over here and since the recipe already calls for flax, do you suggest we use more or something different? Maybe aquafaba? Thanks in advance!

    • Hey Dani! I haven’t tried using aquafaba yet as an egg swap but I’m a biiiiig fan of making flax and chia eggs! I use a flax egg for my banana zucchini flax bread recipe and think flax eggs should work great here as well! I haven’t tested it so I’m not 100% but I’m not sure I’ve ever had a flax egg not work for me, which bodes well! LMK if you get a chance to experiment and how it goes! xoxo

  • Andreea

    Can’t find ground flax. Cand I leave it out? ?

    • Hey Andreea! Of course! It’s a healthy extra that isn’t needed for taste/texture at all so feel free to skip it 🙂

  • Ruby

    Has anyone tried these with gluten-free flour or an alternative like buckwheat? They look delish but my little lady is gluten sensitive.

    • Hi Ruby! I havent made them with gluten-free flours yet but would like to! Do you have a blend that is your go-to? If so I would totally try it out! They might need a bit more moisture as GF flours (coconut for instance) tend to soak up more liquid when baking but the ingredient combo would be fabulous in a GF muffin! Let me know if you end up experimenting and I’ll keep you posted if I get a chance to as well 🙂 xoxo

  • Amanda N

    Can you use a substitute for the almond meal?

    • Hi Amanda! Absolutely! I’ve used extra flax to replace the almond meal numerous times and it works great! Flour should work as a sub too but I haven’t tested that combo yet. 🙂

  • jo

    Could I sub molasses for the maple syrup?

    • Possibly. Are they sweet like syrup or honey? I’m not super familiar with molasses (my mom never kept them in the house) so I’m a little naive on how they work in recipes. I did a little googling and blackstrap molasses are known for being strong and sometimes bitter while the lighter varieties of molasses are less sweet and lighter flavor-wise than honey or syrup. I’m guessing regular molasses may work great texturally but may need a burst of sweetness elsewhere unless you want to make these more on the savory side? I say an experiment is in order! 😉 Let me know what you end up trying! <3 Thanks Jo!

  • Naomi

    5 stars
    These turned out fantastic. I’ll have to keep myself from eating them all. Subs: buckwheat flour for the wheat, china seeds for the flax, and mini muffin tins! 10 minute bake time and a single muffin is a serving for my little man. Also I sped read through the sifting instructions and they turned out plenty fluffy.

  • Colleen

    5 stars
    I have made this a few times and my daughter loves it! Thank you for the recipe. I am not a baker, so I have a question that may be very foolish. I was wondering: does the flour/almond meal mixture have to be sifted? It leaves weird residue in my sifter that I don’t know how to get out, so I was just wondering if I can skip sifting. Thank you for your help!

    • Jenn

      Hey Colleen – thank you so much! I’m so glad she loves the muffins! Sifting just adds to the fluffiness of the muffins but is by no means essential! I would whisk the ingredients together in the bowl with a fork, then sprinkle into the wet mixture slowly as you combine the two. When I’m in a rush I do that method and they’re still great and my toddler devours them all the same! Skip away!

      • Colleen

        Thank you so much for your response. I really appreciate your time!

        • Jenn

          Likewise! I’m lucky to have you as a reader Colleen! 🙂

  • Nicci

    is there any sub for almond meal? Maybe flax? Wanting to just make them nut free

    • Jenn

      Sub Flax or WG flour and you should be good to go! =)

  • 5 stars
    I followed the recipe exactly and these were super moist and delicious! Loved that they were only lightly sweetened- paired perfect with my scrambled eggs this morning!

    • Jenn

      Thanks Kim! I’m so glad you loved them! I was worried adults wouldn’t like the slightly sweetened muffin that I made for the chickpea but so far they’ve been pretty well-received by grown ups too which is the ultimate compliment to please both palates! Thanks so much lady! =)

  • Allison

    This is a silly question, but do you roast the squash before you purée it? I’m excited to make these for the kiddos, I’ve never net a recipe of yours I didn’t love! Thanks!

    • Jenn

      I did! I roast a ton for different recipes [my butternut black bean burgers are one of the uses, SO GOOD!] but it would also be fabulous with steamed and pureed squash or boiled and pureed squash. Even canned will work, they’re super versatile! My toddler is borderline obsessed with them!

  • The smear on the first picture….And I take the chickpeas approval over yours.

  • totally need to try and bake with butternut squash! These look like pure deliciousness! your little one is so adorable! 🙂

  • Claire

    I wanted to share a picture of my little guy (Campbell Jesse, turned 1 last week) – cramming birthday cake into his mouth – because I think he and la demoiselle Chickpea were somehow separated at birth or are destined to one day end up married! I’m excited to make these for him – thanks!

  • Oh this looks so yummy! I think my boyfriend would love these, I knew I made the right choice getting that butternut squash!

  • Oh, I love this! My weird family doesn’t like butternut squash (who ARE they?!) so this is the perfect way to get them to eat some. ‘Cause Lord knows they love them a muffin (or five)!

  • I love healthy inspiration like this! These are a great sneaky way to get the kids to eat their veggies! Pinned!

  • Zucchini? Yeah! Butternut squash? I guess I better try it before I knock it!

    • Jenn

      No knocking needed. My kiddo loves them!

  • Sounds yummy! I believe you on the squash, because I’ve actually toyed with putting zucchini in my oatmeal for zoats before and the flavor is well-masked. Great recipe! Thanks for sharing!

    • Jenn

      Yesssss! Love zucchini in everything! =)

  • These look amazing! Loving all those veggies 😉

    • Jenn

      Danke darling!

  • Oh I love carrot muffins. They are my favorite-est.

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