Gluten Free Pumpkin Carrot Cupcakes

Gluten Free Pumpkin Carrot Cupcakes

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices.

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices.

When the mums are for sale at the grocery store, you know fall is actually around the corner. You certainly can’t go by the wax pumpkins at the hobby store or the Halloween candy for sale. Those can come in the middle of summer. But the mums are the real deal. ?

I’ve been seeing mums for weeks now, so I figure I have the green light to start pushing the pumpkin baking. Besides, soon enough you’ll start hearing that there’s a canned pumpkin shortage coming. Don’t they seem to say that nearly every single year?

These might be the moistest cupcakes I’ve ever made. There’s something about the combination of pumpkin puree, shredded carrots, and oil that just makes for a super tender and moist cake. It’s the sort of cake where the crumbs are so moist they’ll stick to the tines of a fork.

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices.

Are these pumpkin carrot cupcakes … healthy?

I first started making these cupcakes back in 2011. It’s so long ago that my children don’t even remember them.

My oldest asked if they were cupcakes or muffins, which really means she’s asking if she can have them for breakfast. They really are cupcakes, since the batter is relatively thick but the texture is so tender and cake-like.

I’m more likely to call something a muffin if it’s a bit drier and denser. A good muffin is never actually dry, but the crumb is typically a bit drier than a cupcake. A cupcake is, well, a mini cake.

These cupcakes are, in fact, made with 2 cups shredded carrots. Then again, our gluten free carrot cake has plenty of carrots, too, and no one would call that health food.

The batter also has half a can of pure pumpkin puree, which has a single ingredient: pumpkin. There is no denying that these cupcakes are filled with beta-carotene.

But their health benefits, if any, are purely accidental. They’re not a multivitamin, and you wouldn’t really serve them for breakfast (except for a very special occasion?).

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices.

The process

Like most of my cake recipes, these gluten free pumpkin carrot cupcakes are made in one bowl. One notable exception is the very best gluten free vanilla cake recipe, which calls for sifting the flour.

That vanilla cake is a true exception and demands that the butter is beaten with the sugar. The flour must be sifted into the wet ingredients. This cake can be made entirely in one bowl, easily.

All of the ingredients must at room temperature, as is the case for all baking other than pastry-making. If your eggs aren’t already at room temperature, just float them in a warm water bath for about 10 minutes.

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices.

Simply whisk together the dry ingredients (flour, baking soda, salt, spices, granulated sugar, brown sugar), and break up any lumps in the brown sugar. Most of the sugar in this recipe is brown sugar, and it does have a tendency to clump.

Be sure to break up all of those clumps or you’ll have pockets of undissolved sugar in your cupcakes. They’ll bake differently and won’t really become part of the cupcake.

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices.

Next, use a large spoon to create a deep well in the center of the dry ingredients. This will allow the wet ingredients to reach the bottom of the bowl of dry ingredients right away. It makes mixing the batter much easier.

Gluten free cupcakes might not have wheat gluten in them, but tender gluten free baked goods still shouldn’t be overmixed. That’s part of the reason to use melted butter and oil, which allows for faster mixing of the cupcake batter.

Be sure to fill each well of the muffin tin fully with batter. The size of the wells of any muffin tin varies, so if the wells of your muffin tin aren’t quite as large as mine, you’ll end up with some extra batter. Just use it to bake an extra cupcake or two in another pan.

I prefer to line my muffin tins with greaseproof liners (they don’t stick to the baked goods like typical grocery store liners tend to). I find that the batter rises straight up more evenly. But of course you can bake these cupcakes in a greased muffin tin.

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices.

Ingredients and substitutions

Recipe testing isn’t for the faint-of-heart (wasting ingredients is no joke!), and I hate to ask you to do any of it at all. But if I haven’t tried a recipe with certain substitutions, I’m afraid an educated guess is all I can offer. Here goes:

Dairy-free: These cupcakes are really just 1 tablespoon of butter away from being naturally dairy-free. The butter does give the cupcakes some richness, but it’s easily replaced by one extra tablespoon of neutral oil. Just be sure you use dairy-free chocolate chips, and you’re all set!

Egg-free: I’ve never tried these cupcakes with an egg substitute, but I’m tempted to recommend that you try making it with 1 “chia egg” (1 tablespoon ground white chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel) and replacing the second egg with another ounce of pumpkin puree.

I’m afraid I’m just shooting in the dark with that suggestion, though. If you do try it, I’d also try adding 1/4 teaspoon of baking powder to the dry ingredients.

Sugars: The brown sugar in this recipe really gives the cupcakes a richness and depth of flavor that you can’t get from just granulated sugar alone. You can’t replace a granulated sweetener with a liquid one like maple syrup or honey, but you should be able to replace both of the sugars with coconut palm sugar.

Palm sugar is a flavorful, rich unrefined sugar, and can be a great, somewhat healthier alternative to brown sugar. But it doesn’t dissolve quite as well in baking as refined sugars, so I recommend grinding it in a blender or food processor before adding it to the batter. That will help it dissolve.

If you’d like to try an alternative sweetener like monkfruit, I’d recommend trying Swerve brand brown sugar alternative or Lankato monkfruit. Both tend to be drying, though, so you might want to add a bit more pumpkin puree. I’m afraid you’ll have to experiment!

Chocolate chips: When I first started making this recipe years ago, I used to make it with equal amounts white chocolate chips and raisins. But I just love the combination of pumpkin and chocolate so much that I really prefer semi-sweet chocolate chips here now.

If you’d like to replace the chips, though, you can use any small mix-in that holds its shape and doesn’t add moisture. Small bits of dried fruit like raisins are always a solid choice. Chopped nuts would also work really well.

Ease into the baking season with gluten free pumpkin carrot cupcakes, packed with tons of shredded carrots, a cup of pumpkin puree, and plenty of warm spices. #glutenfree #gf #pumpkin #carrotcake #fall #baking

Like this recipe?

Prep time: Cook time: Yield: 12 cupcakes


1 1/2 cups (210 g) all purpose gluten free flour (I used Better Batter)

3/4 teaspoon xanthan gum (omit if your blend already contains it)

1 teaspoon baking soda

1/2 teaspoon kosher salt

2 teaspoons ground cinnamon (or pumpkin pie spice)

1/4 cup (50 g) granulated sugar

1 cup (218 g) packed brown sugar

2 cups (180 g) shredded carrots (from about 5 carrots, peeled and shredded)

1 tablespoon (14 g) unsalted butter, melted and cooled

4 tablespoons (56 g) neutral oil (vegetable, canola or grapeseed)

2 eggs (100 g, weighed out of shell) at room temperature, beaten

7 1/2 ounces pure packed pumpkin (one-half a 15 ounce can)

1 teaspoon pure vanilla extract

4 ounces semi-sweet chocolate chips


  • Preheat your oven to 350°F. Grease or line a 12-cup muffin tin and set it aside.

  • In a large bowl, place the flour, xanthan gum, baking soda, salt, cinnamon, granulated sugar, and brown sugar, and whisk to combine well, working out any lumps in the brown sugar. Add the carrots, and stir to combine. Create a well in the center of the dry ingredients and add the melted butter, oil, eggs, pumpkin and vanilla, and mix to combine. The mixture should be thick and moist, but not at all stiff.  Add most of the chocolate chips, and stir until they’re evenly distributed throughout the batter. If you’d like, reserve a few chocolate chips to place on the tops of the batter once it’s transferred to wells in the muffin tin.

  • Fill the wells of the muffin tin completely with the batter, and shake the tin back and forth to redistribute the batter into even layers in each well. Scatter any remaining chocolate chips evenly over the tops of the dough and press gently to help them adhere. Place the muffin tin in the center of the preheated oven and bake until the muffin tops spring back when they’re pressed gently in the center, about 25 minutes. Allow to cool about 10 minutes in the pan, and then transfer to a wire rack to cool completely.

  • Originally published on the blog in 2011. Recipe tweaked only slightly, images all new, text mostly new. 


Comments are closed.

  • Cristina Moidel
    September 17, 2018 at 9:52 PM

    OMG so good! Thank you for this recipe!

  • Yolanda Carozza
    September 16, 2018 at 3:37 PM

    What store carries the “Better Batter” flour?

    • Nicole Hunn
      September 17, 2018 at 8:04 AM

      I usually buy it directly from their website, Yolanda, but it’s also sold on amazon.com. Just do a quick google search!

  • Heather
    September 13, 2018 at 6:31 AM

    Instead of the canned pumpkin can I use freshly cooked pumpkin processed?

    • Nicole Hunn
      September 13, 2018 at 7:42 AM

      Hi, Heather, definitely! You just want to make sure you roast it as described in this pumpkin butter recipe (you’ll just follow the instructions related to roasting the pumpkin, not adding the other ingredients and making the pumpkin butter), so it has the right amount of moisture. Hope that helps!

  • Karen Langley
    October 7, 2011 at 2:54 PM

    Hey Nicole

    Just made these and they are yummy! They are now my husband’s favorite muffins – and “the second best thing he’s ever tasted.” High compliments.
    The cool thing is that after posting a photo on facebook all my non GF friends want the recipe. The cool thing is I’ll have to say to them “just don’t know if it will convert properly with regular flour!” :)


  • Pamela G
    September 26, 2011 at 10:43 AM

    Scott had just one word…… “Awesome!”

  • PegLeg
    September 26, 2011 at 9:48 AM

    I made these over the weekend and they were soooo good! We ate a total of 3 and then I froze the rest. That’ll keep me from gobbling them down right away. Thanks for the great recipe.

    • Nicole
      September 26, 2011 at 10:16 AM

      Hi, Peggy,
      So glad you enjoyed them! Freezing them wouldn’t really stop me. :)
      xoxo Nicole

  • Tammie
    September 25, 2011 at 6:36 PM

    Thanks for the terrific recipe! I replaced the carrot with zucchini, since we have a surplus of it from our garden, and it turned out really well. Also, to solve the extra batter dilemma, I place it in two greased ramekins and baked them along side the muffins. Later that evening, I whipped up a quick cream cheese frosting and placed a little bit on each ramekin – voila! A nice little surprise for my husband and I after dinner!

    • Nicole
      September 25, 2011 at 11:52 PM

      Hi, Tammie,
      Ooooh interesting! Pumpkin zucchini muffins… You must have really squeezed the water out of that zucchini! I know what it’s like to have to use up garden zucchini. It’s so prolific. It can be really overwhelming. At least I find it overwhelming. Well done! Love the frosting surprise for you and your husband. :)
      xoxo Nicole

  • Kadren
    September 22, 2011 at 7:52 AM

    Oh I think these must be on my agenda today. My kids will LOVE me!!!!!!!!!!!!!!!!!!!!! I do have to mix up a fresh batch of all purpose flour so that’s going to slow me down a touch… Did I mention that I always keep pumpkin in my house? Yup, it’s a staple. :) Pumpkin bread, cake, muffins, bars… even pie occasionally. In a few weeks, I will be heading up 2 days of pie making. Dutch apple and pumpkin, all homemade. Last year we made over 230 pies in one day for our preschool fundraiser. Fun times! :) I might have to make these for our potluck…

    • Nicole
      September 22, 2011 at 12:11 PM

      Hi, Kadren,
      230 pies in one day? As usual, you put me to shame. I have never even made that many pies in a year, much less in a day. In a decade perhaps! I love pumpkin pie from fresh baking pumpkins. Canned pumpkin is great for bars and cakes. For pies, you need the real deal. You’re amazing!
      xoxo Nicole

      • Kadren
        September 22, 2011 at 10:16 PM

        Naw, I was just in charge. There were 6-8 other people there to help. :) And for this, we use canned pumpkin, but we make all crust and everything from scratch. I use my Great Aunt’s apple pie recipe that I tweaked a bit and my mom’s pumpkin recipe. This is our third year making pies and we more than doubled our orders the second year from the first so I set aside 2 days this year in case we end up having to fill a 500 pie order. It would mean some great, much needed money for the preschool! :) And hey, you come up with all these delightful, life saving recipes for all of us, so I’d say you are the best. :)

        • Nicole
          September 23, 2011 at 9:49 AM

          Oh, Kadren, 8 people making hundreds of pies is still the stuff of legends. :)
          xoxo Nicole

  • Peggy
    September 21, 2011 at 8:26 PM

    I should have read the recipe before I went to the store…saw the title with pumpkin so picked up a can of pumpkin but don’t have the carrots…oh well, another trip to the store…still looking for the almond paste so double the reason to make another trip into 90+ degree temps in northern CA. We do love that you love us!!!

    • Nicole
      September 21, 2011 at 9:36 PM

      Hi, Peggy,
      Oh no! I hate that. I think they should put in an automatic revolving door at all my local markets. I frequent them all nearly every other day. It’s 90+ degrees by you, still? I hope that breaks very soon. For almond paste, Whole Foods will have it almost for sure if that’s available to you. I also find that most larger markets carry it.
      xoxo Nicole

  • Laurel Mascia
    September 21, 2011 at 5:10 PM

    My daughter and I made these this afternoon so we could surprise my son when he got off the bus. Everyone loved them!! Thank you!!

    • Nicole
      September 21, 2011 at 5:16 PM

      Hi, Laurel,
      You’re the second person who said she got busy and made these right away. How exciting! I can’t tell you how much fun it is for me to know that. It’s so … 21st Century connected! Love it. So glad you enjoyed. It’s undeniably my pleasure. Your son’s a lucky boy. :)
      xoxo Nicole

  • Joy
    September 21, 2011 at 11:59 AM

    I just made these. Saw your post, checked the pantry for ingredients, and made these. So. Dang. Good!

    • Nicole
      September 21, 2011 at 1:33 PM

      Hi, Joy,
      That’s awesome! Love a good pantry recipe. So glad you enjoyed. So glad you hopped right on ’em!
      xoxo Nicole

  • abby
    September 21, 2011 at 11:44 AM

    YUMMY!!!! I will for sure be making these soon. I make a carrot cake cupcake with organic baby food carrots that my kiddos call “cinnamon” cake and then devour. I don’t correct them as they eat up the lovely carrots. These will be my grown up version that I will eat up – probably for breakfast because they are so healthy :) (I also eat apple pie for breakfast too).

    • Nicole
      September 21, 2011 at 1:34 PM

      Hi, Abby,
      Apple pie for breakfast. A steaming hot cup of coffee, a slice of apple pie, and no children in the house sounds like a Calgon Moment to me. Take me away!
      xoxo Nicole

  • PegLeg
    September 21, 2011 at 11:22 AM

    Will the leftover half-can of pumpkin freeze well? Or should I just make two batches?!?!?

    • Nicole
      September 21, 2011 at 11:27 AM

      Hi, Peggy,
      It keeps well in the refrigerator for a while, and it will also freeze perfectly. You could double the recipe, but you could also make Pumpkin Chocolate Chip Squares (pg. 194 of my cookbook), which calls for 1 cup of pumpkin (7.5 ounces will do just fine). I hope that helps!
      xoxo Nicole

  • September 21, 2011 at 10:35 AM

    Oh.my.word. How incredible do these look? If I can dare say, these little beauties are screaming for cream cheese frosting. I must make these immediately, if not sooner.

    • Nicole
      September 21, 2011 at 10:44 AM

      Hi, Michelle,
      Thanks! When I make carrot cupcakes/muffins, I do indeed make a cream cheese/molasses glaze for them and it’s amazing. These, though. I had every intention of doing it. But I couldn’t pull the trigger. They are so deliciously sweet already. I was afraid. I chickened out. I was afraid to ruin them! Maybe you’re man enough? I’m not. :(
      xoxo Nicole

      • September 21, 2011 at 2:51 PM

        Oh I am sooo man enough. hee hee. Actually I think I may leave out the chocolate chips so I can totally justify the cream cheese frosting. That’s my plan and I’m sticking to it. ; )

        • Nicole
          September 21, 2011 at 3:05 PM

          So impressive, Michelle. I think if you leave out the chips, it’s a go. Otherwise, you might start growing hair on your chest, and nobody wants that. ;)
          Good plan. Well done.
          xoxo Nicole

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