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Gluten Free Chocolate Whoopie Pies Recipe

If you’ve been on the hunt for a crowd-pleasing dessert that’s irresistibly chocolaty but also safe for those avoiding gluten, I absolutely have to share my Gluten Free Chocolate Whoopie Pies Recipe with you. These soft, cake-like cookies sandwich a dreamy, fluffy filling that melts in your mouth, perfect for any occasion from casual afternoons to festive gatherings. Trust me, once you try this recipe, you’ll be making these yummies on repeat.

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Why You’ll Love This Recipe

  • Perfectly Moist & Fluffy: The texture is soft like a cloud and just melts on your tongue every time.
  • Gluten-Free & Allergy-Friendly: This recipe uses a trusty gluten free flour blend and dairy-free ingredients so more people at your table can enjoy it.
  • Rich, Chocolatey Flavor: Unsweetened cocoa powder and coconut sugar create deep chocolate notes without being overly sweet.
  • Incredibly Easy to Make: No fancy equipment or complicated steps — even if you’re not an experienced baker, you’ll have success with this one.

Ingredients You’ll Need

This recipe balances gluten free flours and natural sweeteners carefully to give you moist chocolatey cookies with a creamy, fluffy filling. When shopping, I recommend using a high-quality gluten free all purpose blend and organic coconut sugar if possible for the best flavor.

Flat lay of a small mound of all-purpose gluten free flour blend, a small bowl of glossy tapioca flour, a simple white ceramic bowl filled with rich unsweetened cocoa powder, a small pile of fine baking soda powder, a pinch of coarse sea salt beside it, a smooth round dollop of golden ghee, a small heap of granular coconut sugar, one large whole brown egg with a clean shell, a small white bowl of amber maple syrup, a teaspoon of clear vanilla extract in a tiny white bowl, a small white bowl with creamy canned coconut milk, another small white bowl with smooth dairy-free coconut milk, a small white bowl heaped with sifted powdered sugar, and a round chunk of pale palm shortening—all arranged symmetrically with perfect spacing, placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997 - Gluten Free Chocolate Whoopie Pies, gluten free dessert recipes, chocolate sandwich cookies, dairy free gluten free treats, easy gluten free desserts
  • Gluten free all purpose flour blend: I use Bob’s Red Mill 1-to-1, it has great structure for baked goods.
  • Tapioca flour: Helps soften the texture and gives a bit of chew.
  • Unsweetened cocoa powder: Choose a good quality brand for deep chocolate flavor.
  • Baking soda: The leavener that helps the cookies puff up perfectly.
  • Sea salt: Just a pinch brings out all the flavors beautifully.
  • Ghee: Adds richness and moisture while being dairy-free friendly.
  • Coconut sugar: Gives a slight caramel note that pairs amazingly with chocolate.
  • Large egg: For binding and structure.
  • Maple syrup: Adds natural sweetness and moisture.
  • Vanilla extract: For warmth and enhanced flavor.
  • Canned coconut milk: Adds creaminess without dairy.
  • Dairy-free milk: I usually use extra coconut milk for richness.
  • Powdered sugar: Sifted for a silky smooth filling.
  • Palm shortening: Keeps the filling light and fluffy but stable for piping.
Note: You’ll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Variations

I love making this recipe my own depending on the occasion or who I’m baking for. The core recipe is so versatile—here are some tweaks you might want to try to suit your tastes or dietary needs.

  • Spiced Chocolate: I sometimes add a teaspoon of cinnamon or a pinch of cayenne to the batter for a cozy, unexpected kick that my family adores.
  • Nut-Free Filling: To keep these completely nut-free, make sure to use palm shortening and check your dairy-free milks are allergen safe.
  • Chocolate Ganache Filling: If you want to mix it up, swap the frosting for a simple coconut cream chocolate ganache—so decadent!
  • Mini Whoopie Pies: For parties, I halve the scoop size to create bite-sized whoopie pies that fly off the platter.

How to Make Gluten Free Chocolate Whoopie Pies Recipe

Step 1: Prep Your Workspace and Ingredients

First thing’s first—preheat your oven to 350°F and line two large baking sheets with parchment paper. I like to have everything measured and ready because gluten free baking is all about timing and texture. Whisk together the gluten free flour blend, tapioca flour, cocoa powder, baking soda, and salt in a medium bowl and set aside. This dry mix is the backbone of your cake-like cookies, so get those lumps out now!

Step 2: Mix the Batter

Using a stand mixer or hand mixer fitted with the paddle attachment, beat the room temperature ghee and coconut sugar together until creamy. Then add the egg and beat until fully combined—this helps make your cookies tender and moist. Mix in the maple syrup, vanilla extract, and canned coconut milk until everything’s smooth. Finally, add your dry ingredients and mix on low speed until your batter is smooth and thick, like a well-blended cake batter. Don’t over mix here to keep things tender.

Step 3: Scoop and Bake

Grab a spring-loaded 2 tablespoon cookie scoop to portion out uniform rounds of batter onto your parchment-lined sheets. I space mine about two inches apart because these babies puff up just right. You should get about 24 cookies total. Bake for 10-12 minutes until the tops puff up and spring back lightly when you press the center. This part is crucial: don’t over bake or your whoopie pies can dry out. Cool them completely on a wire rack before filling.

Step 4: Whip the Filling

In a large pourable container, combine the coconut milk and sifted powdered sugar until smooth. Then, with your mixer, beat the palm shortening until it’s silky and smooth, about 1-2 minutes. Add vanilla extract and mix again. Slowly drizzle in the milk and powdered sugar mixture and whip everything together until the frosting is light, fluffy, and clump-free. It’s like catching a cloud with your spoon!

Step 5: Assemble Your Whoopie Pies

Fit a piping bag with a large round tip and fill it with that dreamy frosting. Pipe a generous dollop on the flat side of half your cookies, then gently place a second cookie on top, flat side down, twisting slightly to secure. These are best served fresh, but you can refrigerate for later.

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Pro Tips for Making Gluten Free Chocolate Whoopie Pies Recipe

  • Use Room Temperature Ingredients: I always make sure my ghee and eggs are at room temp to help the batter come together beautifully.
  • Don’t Skip Sifting: Sifting the cocoa and powdered sugar avoids clumps and gives a smoother texture to cookies and filling.
  • Watch Oven Time Closely: I set a timer for 10 minutes and check my cookies; overbaking dries them out fast.
  • Gentle Assembly: When sandwiching, twist gently to avoid cracking your cookies—this little trick preserved my first batch perfectly!

How to Serve Gluten Free Chocolate Whoopie Pies Recipe

A close-up of several sandwich cookies stacked and lying in a white bowl, each cookie has two round dark brown chocolate layers with a thick light cream filling in the middle; the top cookie is bitten, showing the soft texture inside. In the background, there is a tall clear glass jug and a glass of white milk against a white marbled texture. The overall scene is softly lit, highlighting the texture and color contrast of the cookies and cream filling. Photo taken with an iphone --ar 2:3 --v 7 - Gluten Free Chocolate Whoopie Pies, gluten free dessert recipes, chocolate sandwich cookies, dairy free gluten free treats, easy gluten free desserts

Garnishes

I usually keep it simple with a light dusting of powdered sugar or a few chocolate shavings on top for a touch of elegance. Sometimes I add a sprinkle of toasted coconut flakes on the filling just before sandwiching for a subtle crunch and extra flavor.

Side Dishes

My favorite pairings with these whoopie pies are a big cup of homemade chai tea or rich coffee—they balance the sweetness perfectly. For a brunch spread, serving alongside fresh berries or a crisp green salad adds a refreshing contrast.

Creative Ways to Present

For parties, I’ve arranged mini whoopie pies on a tiered cake stand with edible flowers for a whimsical touch. Another time, I wrapped each pie in parchment with a pretty ribbon to give as homemade gifts—it was a total hit!

Make Ahead and Storage

Storing Leftovers

I store leftover whoopie pies in an airtight container in the fridge for up to 4 days. I find the filling holds its fluffiness well, and the cookies stay soft if you keep them sealed properly.

Freezing

These whoopie pies freeze beautifully! I wrap each pie individually in plastic wrap and place them in a freezer bag. When I want one, I let it thaw overnight in the fridge. The texture stays just as good as fresh.

Reheating

If I want to enjoy a warm whoopie pie, I pop it in the microwave for about 10 seconds—just enough to soften the filling but not melt it completely. It’s like a cozy little hug in dessert form.

FAQs

  1. Can I use a different gluten free flour blend?

    Absolutely! I recommend a 1-to-1 gluten free baking flour that includes xanthan gum or guar gum for structure, but you can experiment with your favorite blends. Just keep in mind that texture might slightly vary between brands.

  2. What’s the best way to make the filling dairy-free?

    This recipe uses palm shortening and coconut milk to keep the filling dairy-free, and it works wonderfully. Avoid butter or cream cheese if you’re after a fully dairy-free treat.

  3. Can I make these whoopie pies in advance?

    Yes! You can bake the cookies ahead of time and store them separately in an airtight container. Assemble with filling the day you want to serve for the freshest experience.

  4. What if I don’t have palm shortening?

    I’ve tried swapping with vegan butter, but palm shortening gives the best light and stable texture. If using vegan butter, make sure it’s solid and cold, then whip it well to achieve fluffiness.

  5. How do I prevent the cookies from cracking when sandwiching?

    When assembling, gently twist the top cookie onto the filling rather than pressing straight down. This little trick keeps the cookies from cracking and makes the whole pie look pretty.

Final Thoughts

This Gluten Free Chocolate Whoopie Pies Recipe holds a special place in my kitchen because it delivers comfort and joy every time. Whoever I share them with ends up asking for seconds, and that’s a sign of a keeper dessert. If you’ve been wanting a reliable gluten free chocolate treat that doesn’t feel like a compromise, give this a try—you’ll find it’s easier than you think, and the results are simply divine.

Print
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Gluten Free Chocolate Whoopie Pies Recipe

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.9 from 59 reviews
  • Author: Lisa
  • Prep Time: 25 minutes
  • Cook Time: 12 minutes
  • Total Time: 37 minutes
  • Yield: 12 whoopie pies 1x
  • Category: Dessert
  • Method: Baking
  • Cuisine: American
  • Diet: Gluten Free

Description

Delicious gluten free whoopie pies made with a blend of gluten free flours, cocoa powder, and a rich, creamy dairy-free filling. These soft, chocolatey treats are perfect for those avoiding gluten and dairy without sacrificing flavor or texture.


Ingredients

Scale

Dry Ingredients

  • 1 ¼ cup all purpose gluten free flour blend (Bob’s Red Mill 1-to-1 Gluten Free Baking Flour)
  • ½ cup tapioca flour
  • ½ cup unsweetened cocoa powder
  • 1 ¼ teaspoons baking soda
  • ¼ teaspoon sea salt

Wet Ingredients for Cake

  • ½ cup ghee, room temperature
  • ¾ cup coconut sugar
  • 1 large egg
  • ¼ cup maple syrup
  • 1 teaspoon vanilla extract
  • ¾ cup canned coconut milk

Filling Ingredients

  • ¼ cup dairy-free milk (coconut milk recommended)
  • 2 cups powdered sugar, sifted
  • ¾ cup palm shortening
  • 1 teaspoon vanilla extract

Instructions

  1. Preheat Oven and Prepare Pans: Preheat your oven to 350°F (175°C) and line two large baking sheets with parchment paper to prevent sticking and ensure even baking.
  2. Whisk Dry Ingredients: In a medium bowl, combine the gluten free flour blend, tapioca flour, unsweetened cocoa powder, baking soda, and sea salt. Whisk thoroughly to blend all the dry ingredients evenly and set aside.
  3. Mix the Batter: Using a stand or hand mixer fitted with the paddle attachment, beat the room temperature ghee and coconut sugar together until creamy. Add the egg and mix until fully incorporated. Then add the maple syrup, vanilla extract, and canned coconut milk, mixing until combined. Gradually add the dry ingredient mixture and mix on low speed until the batter is smooth and thick.
  4. Scoop the Batter: Using a 2-tablespoon spring-loaded cookie scoop, portion the batter onto the prepared baking sheets, spacing each mound about two inches apart. This should make approximately 24 cookies.
  5. Bake the Cookies: Place the baking sheets in the oven and bake for 10 to 12 minutes, or until the dough cakes puff up and spring back lightly to the touch. Remove from oven and transfer the cookies to a wire rack to cool completely.
  6. Prepare the Filling: In a large pourable measuring cup, mix the dairy-free milk and sifted powdered sugar until smooth. In a separate bowl, beat the palm shortening with a mixer for 1 to 2 minutes until creamy. Add vanilla extract and incorporate. Slowly add the milk and powdered sugar mixture to the shortening, beating continuously until the filling is light, fluffy, and free of lumps, about 2 to 3 minutes.
  7. Assemble Whoopie Pies: Transfer the filling to a piping bag fitted with a large round tip. Pipe a generous amount of filling onto the flat underside of 12 cookies. Carefully top each with one of the remaining cookies, flat side down, and gently twist to secure.
  8. Serve or Store: Serve immediately or store the whoopie pies in an airtight container in the refrigerator for up to 4 days to maintain freshness and texture.

Notes

  • Ensure ghee is at room temperature for easier mixing.
  • Use a properly sifted powdered sugar to avoid lumps in the filling.
  • Space cookies adequately on baking sheet to allow for spreading.
  • Allow cookies to cool completely before assembling to prevent melting the filling.
  • Store assembled whoopie pies refrigerated and consume within 4 days.
  • Substitute palm shortening with vegetable shortening if unavailable.

Nutrition

  • Serving Size: 1 whoopie pie
  • Calories: 320
  • Sugar: 22g
  • Sodium: 150mg
  • Fat: 18g
  • Saturated Fat: 9g
  • Unsaturated Fat: 8g
  • Trans Fat: 0g
  • Carbohydrates: 38g
  • Fiber: 3g
  • Protein: 3g
  • Cholesterol: 20mg

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