Gluten Free Carrot Cake Whoopie Pies

Gluten Free Carrot Cake Whoopie Pies

These moist and tender gluten free carrot cake whoopie pies with cream cheese filling are a fun Easter alternative to cupcakes or cake. And they freeze great!

These moist and tender gluten free carrot cake whoopie pies with cream cheese filling are a fun Easter alternative to cupcakes or cake. And they freeze great!

What is it about carrot cake?

I don’t know anyone who doesn’t like carrot cake. Do you? The way I make carrot cake, there are plenty of shredded carrots—but even if you don’t like carrots (like my oldest, who hates all vegetables equally, poor kid), you must like carrot cake. There’s something about the marriage of cream cheese with carrots that don’t really even taste like carrots-for-salad with cinnamon and, for me, a hint of freshly grated nutmeg.

This recipe really does round out my carrot cake repertoire. I have the classic gluten free carrot cake recipe all wrapped up, plus the Entenmann’s-style carrot cake with crushed pineapple in the batter, too.

These moist and tender gluten free carrot cake whoopie pies with cream cheese filling are a fun Easter alternative to cupcakes or cake. And they freeze great!

I went a little bit light on the confectioners’ sugar in the cream cheese filling. If you add more confectioners’ sugar, you will get a more stable filling. But it will threaten to overwhelm the other flavors in these gluten free carrot cake pies with an overwhelming rush of pure sweetness. As it is, these pies do best when they are chilled until the filling is firm.

These moist and tender gluten free carrot cake whoopie pies with cream cheese filling are a fun Easter alternative to cupcakes or cake. And they freeze great!


I’ve read all sorts of explanations for the moniker “whoopie pies,” but the one that sticks out for me is that children would see them in their lunchboxes and call out “WHOOPIE!” That has to be the sorriest excuse for a silly naming story I’ve ever heard in my entire life.

I tend to like cupcakes more than cake, but that might be because a cake just doesn’t make for very convenient leftovers. The shredded carrots here tend to rob these cakes of the perfect dome shape of a more classic whoopie pie. But they’re still light, fluffy and tender as can be.

These moist and tender gluten free carrot cake whoopie pies with cream cheese filling are a fun Easter alternative to cupcakes or cake. And they freeze great!

I use a pastry bag fitted with a large plain piping tip for everything from the pies themselves to piping in the filling. But you can easily get away with just spooning both the batter for the cakes and the filling between them.

These moist and tender gluten free carrot cake whoopie pies with cream cheese filling are a fun Easter alternative to cupcakes or cake. And they freeze great!

Watch this short (1:19) how-to video.

Push play ▶ below to watch me make these sweet little cakes, and then make your own!


Ingredients and substitutions

Dairy-free: I’m happy to report that I’ve successfully made the whoopie pies plus the cream cheese filling dairy-free. 🎉 For the cakes, the only dairy-containing ingredient is the melted and cooled butter, and potentially the milk.

For the butter, I feel pretty confident that you can use any vegan butter replacement. I’ve used both Earth Balance buttery sticks and Melt brand vegan butter sticks (which I love love love). For the milk, any unsweetened milk replacement that isn’t fat-free and isn’t, say, a super high-fat can of coconut milk, will work just fine. My favorite is unsweetened almond milk.

For the filling, I recommend using only 2 ounces of your favorite dairy-free cream cheese, since I find that all of them have something of a strange aftertaste, 4 tablespoons (56 g) of vegan butter replacement like Melt or Earth Balance, and 4 tablespoons of shortening. Speaking of shortening…

Shortening: If you see shortening as an ingredient in a recipe and want to turn the virtual page, please hear me out! Shortening, unlike butter or vegan butter replacements, is solid at room temperature but has little to no moisture (unlike butter, vegan or otherwise). It helps baked goods stay put and not spread too much in the oven, and frosting to hold its shape.

I don’t buy or use Crisco. I recommend Spectrum nonhydrogenated vegetable shortening, which is much heathlier for you and sustainably sourced. To replace shortening, you can try using virgin coconut oil (the triple filtered kind has no coconut aroma), but it won’t always work exactly the same.

Egg: Since there is only one egg in this recipe, I think a “chia egg” (1 tablespoon of ground chia seeds + 1 tablespoon of lukewarm water, mixed and allowed to gel), but if you’re feeling adventuresome and want to try a boiled flax egg like we did in our vegan black bean brownies, that would work great.

Sugar: You cannot replace the brown and confectioners’ sugars in this recipe with a liquid sweetener of any kind. You should be able to replace the brown sugar with coconut palm sugar, but I’d recommend grinding it further so it dissolves properly during baking.

For an entirely sugar-free recipe, you can try replacing the brown sugar with Swerve brown sugar replacement or even Lankato brand (I’ve just started experimenting with that; nothing to report just yet!), but those sugar replacements tend to absorb more moisture so you might have to add more milk. For the confectioners’ sugar, you’ll need Swerve confectioners’ sugar replacement.

These moist and tender gluten free carrot cake whoopie pies with cream cheese filling are a fun Easter alternative to cupcakes or cake. And they freeze great!

Like this recipe?

Prep time: Cook time: Yield: 10 whoopie pies


For the cakes
1 1/4 cups (175 g) all purpose gluten-free flour (I like Better Batter or mock Better Batter here)

1/2 teaspoon xanthan gum (omit if your blend already contains it)

1/2 teaspoon baking powder

1/4 teaspoon baking soda

1/4 teaspoon kosher salt

1 teaspoon ground cinnamon

1/4 teaspoon freshly grated nutmeg

1/2 cup (109 g) packed light brown sugar

1 1/3 cups (120 g) freshly grated carrots (about 2 medium carrots)

2 tablespoons (28 g) unsalted butter, melted and cooled

2 tablespoons (24 g) vegetable shortening, melted and cooled

1 teaspoon pure vanilla extract

1 egg (50 g, weighed out of shell) at room temperature, beaten

1/2 cup + 2 tablespoons (5 fluid ounces) milk (any kind), at room temperature

For the filling
6 ounces cream cheese, at room temperature

4 tablespoons (56 g) unsalted butter, at room temperature

1 1/2 cups (173 g) confectioners’ sugar

1/8 teaspoon kosher salt

1/4 teaspoon freshly grated nutmeg


  • Preheat your oven to 350°F. Line rimmed baking sheets with unbleached parchment paper and set them aside.

  • In a large bowl, place the flour, xanthan gum, baking powder, baking soda, salt, cinnamon, nutmeg and brown sugar and whisk until well-combined, making sure to work out any lumps in the brown sugar. Add the grated carrots and mix to combine. Add the butter, shortening, vanilla, egg and milk, and mix until just combined. The batter should be smooth and thick, but soft.

  • Transfer the batter to a large pastry bag fitted with a large plain tip. Pipe rounds about 2-inches in diameter about 1 1/2 inches apart on the prepared baking sheets. With wet fingers smooth and flatten the rounds until they are about 2-1/2 inches in diameter and about 1/2-inch thick. Repeat with the remaining batter.

  • Place the baking sheet in the center of the preheated oven and bake until the cakes are very lightly golden brown all over, and the center springs back when pressed lightly with your finger (about 12 minutes). Remove from the oven and allow to cool completely on the baking sheet.

  • While the cakes are cooling, make the filling. In the bowl of a stand mixer fitted with the paddle attachment, place the butter and cream cheese, and mix on medium-high speed until light and fluffy. Add the confectioners’ sugar, salt, and nutmeg, and mix until all of the sugar is absorbed and the filling has thickened.

  • Once the pies are completely cool, place them in pairs of similar shape and size. Place the filling in a clean pastry bag fitted with a clean large, plain tip, and pipe filling onto the underside of one pie of each pair, stopping just short of the edge of the pie. Cover the filling with the other pie in each pair, and press down gently to force the filling to the edge of the pie. Chill until the filling is firm. Serve slightly chilled.

  • Wrap each leftover pie individually, and store in an airtight container in the refrigerator for 3 or 4 days. Freeze for longer storage.

  • Originally published in 2012 (!). Recipe mostly unchanged (nutmeg added to filling), photos, video and most text new. 


Comments are closed.

  • Maureen
    March 18, 2018 at 9:21 AM

    Good Morning! Your recipe looks amazing, but I have a nephew who can’t eat dairy, eggs…so I will make them “naked” …can I sub applesauce for the egg? Thanks Maureen

    • Nicole Hunn
      March 18, 2018 at 9:25 AM

      Hi, Maureen, Please read the post to the end! I have a whole section on “Ingredients and Substitutions” and it explains all of my recommendations for all the other allergens. Enjoy!

  • Mimk
    March 18, 2018 at 12:13 AM

    when you say they freeze great, do you mean frozen raw or baked? Ive never thought to freeze baked goods and it’s a great idea

    • Nicole Hunn
      March 18, 2018 at 9:26 AM

      Oh my gosh, Mimk, I often freeze baked goods! You’re in for a treat. The refrigerator tends to alter moisture and flavor content (and not for the better), but placing well-wrapped and sealed baked goods in the freezer kind of arrests time! They freeze great as baked and even filled.

  • VT
    October 1, 2012 at 9:17 AM

    I made these over the weekend. My chocoholic kid didn’t like ’em, but my chocohater kid actually said “UMMMM!” on the very first bite. Have to tell ya, it was thumbs up on the naked whoop, without the cream cheese inside. So, guess I now have a carrot cookie recipe! 

    Btw, you scared the bejezus out of me – the email subject line “Last Week on the Shoestring” made me think “OMG, she’s quitting????” Whew, thank goodness I was wrong. I own your first book, your new book is preordered, and I can’t wait for the next one.

    • gfshoestring
      October 1, 2012 at 2:20 PM

      Hi, VT,
      I had never read the “Last Week on the Shoestring” subject line like that before, but now that you say it, I can see how it would seem like the very last week! Nope. Not to worry. I’m not going anywhere. :)
      And I giggled at “naked whoop,” since I’m not very mature. Thank you for your support of the books!
      xoxo Nicole

  • Melissa
    September 25, 2012 at 12:37 PM

    Any way to do these with out the cream cheese filling? I am dairy free, gluten free and sugar free. So maybe I should just avoid the whole recipe :(  Melissa

  • September 24, 2012 at 7:09 PM

    please open a small gluten free bakery in my town! Rockwall Texas…..PLEASE!

    • gfshoestring
      September 25, 2012 at 1:52 PM

      I suspect that you would really prefer I open a very, very small gluten-free bakery in your kitchen, Sheriff. ;)
      xoxo Nicole

  • RebeccaLB
    September 24, 2012 at 12:37 PM

    These sound heavenly! And I agree that the whole point of carrot cake is the marriage of cream cheese with the subtle spices and the sweetness of cooked carrots in the cake.  This maybe my new favorite. 

    • gfshoestring
      September 25, 2012 at 1:55 PM

      Oh indeed, Rebecca. Big time fave of mine.
      xoxo Nicole

  • Rocky
    September 24, 2012 at 12:17 PM

    Awesome looking whoopie pies. Do you think we could use a muffin top pan for the cookie part? I have them sitting in the cupboard and haven’t used them much. Thanks….Love all you do for us:)

    • gfshoestring
      September 25, 2012 at 1:53 PM

      Hi, Rocky,
      If you wanted to use the muffin top pan, I assume you could just make some really, really large whoopie pies. Whoopie indeed. ;)
      xoxo Nicole

  • Pinkpeppercornandpaprika
    September 24, 2012 at 11:08 AM

    What a great twist on the classic whoopie pie! I bet a pumpkin flavored cookie would taste amazing as well! With maybe a chocolate cream cheese filling.

  • cpw
    September 24, 2012 at 10:19 AM

    Hmmm, could this recipe be used to make plain ol’ carrot cake, too?  Or do you already have a recipe for the cake that I missed?

  • lettergirl
    September 24, 2012 at 9:47 AM

    I’m pretty sure I could grate that carrot so incredibly fine that even my cooked-carrot-hating daughter would eat these.  Cream cheese filling, yum!  Gina

    • gfshoestring
      September 24, 2012 at 10:26 AM

      Oh, no doubt, Gina. Who can complain, anyway, with cream cheese filling?
      xoxo Nicole

  • Anneke
    September 24, 2012 at 9:40 AM

    Well, I guess even best friends have to disagree on something . . .  no carrot cake for me!  I have tried it so many times, because it seems like something I should love, but I just don’t.  I know we can still be besties, though, ’cause you don’t judge.  Frankly, I am always a little relieved when a recipe shows up on the blog that I am not going to make, since I am so busy making bread and breakfast cookies and muffins to keep my kids in lunch and breakfast food that I don’t really have time for something new!  Hope you have a beautiful fall day today!


    • gfshoestring
      September 24, 2012 at 10:28 AM

      I wonder if maybe the only carrot cake you have had, Anneke, is one with shredded coconut buried in it. I love coconut chips, but despise stringy shredded coconut, and oddly it is a common ingredient in carrot cake. For me, it threatens to ruin the whole shebang. No worries, though, if I’m totally off-base. Continue baking muffins and breakfast cookies and bread. And rest up for the new book in just a few weeks. ;)
      Your Best Friend,

      • Pinkpeppercornandpaprika
        September 24, 2012 at 11:10 AM

        Or maybe a carrot cake with raisins. That’s what often ruins it for me!

      • Anneke
        September 24, 2012 at 2:54 PM

        I tell you, Nicole, I have eaten every recipe known to man, from bakeries to my grandmother’s — coconut, raisins, nuts, or none of the above.  I think maybe it is a defective gene!  Resting up as much as possible for the new book, and pretty darned excited about the breads coming in book 3!

        • gfshoestring
          September 25, 2012 at 1:57 PM

          I’m so glad you’re excited about the bread book, Anneke! I’m rather excited about it myself, which is good since the manuscript is due April 15, 2013. ;)
          You are officially carrot-cake-broken. I give up!
          xoxo Nicole

  • September 24, 2012 at 9:04 AM

    These look divine. ‘Nuff said. ;)

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