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Prepare to fall in love with these Red Velvet Whoopie Pies! Far from your average treat, these delightful little bites are a celebration of flavor and mindful baking. Each pie features soft, cake-like cookies embracing a luscious, creamy filling – a truly irresistible combination. What makes them even more special is their natural coloring, free from artificial dyes, and their commitment to diverse dietary needs: they’re entirely Paleo, Gluten-Free, Dairy-Free, and AIP-friendly. Get ready to bake a batch of guilt-free indulgence that’s perfect for any occasion, from a romantic Valentine’s treat to a satisfying everyday dessert.

The Charm of Whoopie Pies: A Timeless Treat Reimagined
Whoopie pies hold a special place in the hearts of dessert lovers, offering the best of both worlds: the chewiness of a cookie and the moistness of a cake, perfectly paired with a rich, creamy center. I’ve long dreamed of crafting a version that caters to a wider audience without compromising on taste or texture. This recipe is the culmination of that desire, transforming a classic into a modern, health-conscious masterpiece. Whether it’s for Valentine’s Day, a birthday, or simply a Tuesday craving, these mini whoopie pies are an ideal treat to share with family and friends, or to keep all to yourself!
Traditional red velvet desserts often achieve their signature vibrant hue through artificial food colorings, which many prefer to avoid. This recipe, however, takes a different approach by harnessing the natural power of a humble superfood: beets. Now, before you hesitate, let me reassure you – these whoopie pies absolutely do NOT taste like beets. The beet’s primary role here is to impart that beautiful, authentic red color, while subtle cocoa notes and the sweetness of maple syrup create the classic red velvet flavor profile. The result is a sweet, creamy, and visually stunning dessert, completely free from artificial colors or flavors.

Why Choose Mini Whoopie Pies? Size Matters for Perfection
You’ll notice that this recipe yields adorable mini whoopie pies, and there’s a good reason for this design choice. Smaller pies are not only charming and easy to portion, but they also hold their shape beautifully, making them less prone to crumbling and easier to handle. This miniature size also means there are more to share (or to savor over time!). While I’ve exclusively prepared them as minis, I believe the recipe should adapt well to larger whoopie pies, though baking times may need slight adjustments. The key is to achieve that perfect soft, cakey cookie that cradles the rich filling without falling apart.
Meeting Diverse Dietary Needs: Paleo, Gluten-Free, Dairy-Free, and AIP
One of the standout features of these red velvet whoopie pies is their incredible adaptability to various dietary requirements. They are:
- Paleo-Friendly: Made with wholesome, unrefined ingredients like coconut flour, arrowroot starch, palm shortening, and natural sweeteners, these pies align perfectly with paleo principles.
- Gluten-Free: By using a careful blend of coconut flour and arrowroot starch, we eliminate gluten entirely, making them safe for those with gluten sensitivities or celiac disease.
- Dairy-Free: The recipe uses palm shortening for both the cookies and the luscious cream filling, ensuring a completely dairy-free indulgence.
- AIP (Autoimmune Protocol) Compliant: With the simple substitution of carob powder for cocoa powder, these whoopie pies fit seamlessly into an AIP elimination phase, offering a delightful treat for those navigating autoimmune health.
This makes them an excellent choice for parties or gatherings, ensuring everyone can enjoy a delicious dessert without compromise.
The Essential Ingredients for Your Red Velvet Whoopie Pies
Crafting these delectable whoopie pies relies on a handful of key ingredients, each playing a crucial role in achieving the perfect texture, flavor, and vibrant color. Here’s a detailed look at what you’ll need:
Coconut Flour & Arrowroot Starch: The Gluten-Free Foundation
This dynamic duo forms the gluten-free base for our whoopie pie cookies. Coconut flour, known for its high fiber content and unique absorbency, provides a tender crumb and a subtle sweetness. Arrowroot starch, a fantastic grain-free thickener, contributes to the cookies’ soft, cake-like texture. It’s important to note that coconut flour is very absorbent, so accurate measurement is key. While tapioca starch can generally be substituted for arrowroot starch in equal measure, coconut flour is unique and I do not recommend swapping it for another flour in this recipe to ensure the desired outcome.
A Small Beet: Nature’s Perfect Dye
As mentioned, the secret to the stunning red hue is a small beet. Don’t let this ingredient deter you! When properly prepared, the beet’s earthy flavor completely disappears, leaving behind only its beautiful crimson pigment. The process involves boiling the beet until tender, then pureeing it into a smooth paste. This simple step transforms your whoopie pies into a visual masterpiece without relying on artificial colors, and it even adds a touch of hidden nutrition.
Cocoa Powder (or Carob for AIP): The Rich Flavor Enhancer
Cocoa powder plays a dual role in this recipe. Firstly, it provides the quintessential “red velvet” flavor, a subtle chocolatey note that complements the sweetness. Secondly, it cleverly helps to mask any potential faint beet flavor, ensuring a purely delicious experience. For those following the Autoimmune Protocol (AIP), carob powder is an excellent substitute, offering a similar depth of flavor that is well-suited for AIP recipes.
Palm Shortening: For Structure and Creaminess
Palm shortening is a star ingredient here, crucial for both the cookie’s structure and the filling’s luxurious creaminess. In the cookies, it helps create that desirable cakey texture. In the filling, it forms the rich, stable base that mimics traditional cream cheese frosting, but in a dairy-free and AIP-friendly form. Ensure you use a high-quality, sustainably sourced palm shortening for the best results.
Maple Syrup/Honey: The Natural Sweeteners
You have options for sweetening these treats! Maple syrup is ideal if you’re making these whoopie pies vegan, offering a distinct, rich sweetness. Honey, on the other hand, can also be used and tends to give the cream filling a slightly lighter, brighter color, which can be lovely. Both are natural, unrefined sweeteners that fit within paleo and AIP guidelines.

Mastering the Recipe: Step-by-Step Instructions for Perfect Whoopie Pies
Crafting these delightful red velvet whoopie pies is a straightforward process, but paying attention to each step ensures the best outcome. Here’s how to bring these treats to life:
Preparing the Beet Puree: The Secret to Natural Color
- Begin by placing your peeled small beet in a medium-sized pot and covering it generously with water.
- Bring the water to a gentle boil, then reduce heat and simmer for approximately 25-30 minutes, or until the beet is fork-tender and easily pierced.
- Once cooked, drain the excess water and let the beet cool completely. This cooling step is important for blending.
- Transfer the cooled beet to a blender or food processor. Puree until completely smooth. If needed, add just 1 tablespoon of water to help it blend into a silky paste. You will only need 2 tablespoons of this vibrant puree for the cookies. Any leftover beet puree can be stored and used in smoothies or soups for a nutrient boost!
Baking the Cakey Cookies: Achieving the Perfect Texture
- Preheat your oven to 350°F (175°C). Line a baking sheet with parchment paper, lightly greasing the paper for easy removal.
- In a medium-sized bowl, combine the dry ingredients for the cookies: coconut flour, arrowroot starch, cocoa powder (or carob powder for AIP), and baking soda. Whisk them together thoroughly to ensure even distribution.
- Add the prepared beet puree, palm shortening, and maple syrup (or honey) to the dry ingredients. Stir everything together until a cohesive, well-combined dough forms. The dough will be thick.
- Scoop out approximately 1 tablespoon of cookie dough for each whoopie pie. Place each scoop onto the prepared baking sheet and use the palm of your hand to gently flatten it into a uniform cookie shape. Aim for about 12 cookies, which will yield 6 whoopie pies.
- Bake in the preheated oven for 10 minutes. The cookies will be soft.
- Carefully transfer the baked cookies to a wire cooling rack. It is crucial to allow them to cool completely before attempting to handle them or assemble the pies, as they are delicate when warm and can break easily.
Whipping Up the Creamy Filling: The Heart of the Whoopie Pie
- While the cookies are cooling, prepare your luscious cream filling. In a bowl, combine the softened palm shortening and your chosen sweetener (honey or maple syrup).
- Whisk the ingredients together vigorously until light, fluffy, and well combined. If using an electric mixer, beat on medium speed for 2-3 minutes until the mixture is airy and smooth.
Assembling Your Whoopie Pie Masterpiece
- Once the cookies are completely cool, spoon a generous amount of cream filling onto the flat bottom of one cookie.
- Gently sandwich it with another cookie, pressing lightly to secure the filling. Repeat this process for the remaining cookies, creating 6 beautiful whoopie pies.
- For the best frosting consistency and to allow the flavors to meld, I recommend chilling the assembled whoopie pies in the refrigerator for at least 30 minutes before serving. If you can’t wait, they can also be enjoyed immediately for a softer, melt-in-your-mouth frosting.
Tips for Whoopie Pie Success
- Beet Prep is Key: Ensure your beet is thoroughly cooked and pureed without any lumps. A smooth puree ensures even color and no discernible texture in your cookies.
- Measure Accurately: Especially with gluten-free flours like coconut flour, precise measurements are crucial for the right cookie consistency.
- Don’t Overbake: The cookies should remain soft and slightly cakey. Overbaking can lead to dry whoopie pies.
- Cool Completely: Patience is a virtue here. Warm cookies will absorb the filling or break when handled.
- Filling Consistency: If your palm shortening is too firm, gently soften it at room temperature or for a few seconds in the microwave (be careful not to melt it). If it’s too soft, chill it slightly before mixing.
- Storage: Store leftover whoopie pies in an airtight container in the refrigerator for up to 3-4 days. They are best enjoyed slightly chilled.

Red Velvet Whoopie Pies (Paleo, Vegan, AIP, Gluten Free)
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Ingredients
For the whoopie pies
- 1 small beet, peeled
- ½ cup coconut flour
- ¼ cup arrowroot starch
- 1 tbsp cocoa powder, sub carob powder for AIP
- ½ tsp baking soda
- ¼ cup + 2 tbsp palm shortening
- ¼ cup maple syrup
For the cream filling
- ⅓ cup palm shortening
- 1 tbsp light colored honey/maple syrup for vegan, see notes
Instructions
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Add the beet to a medium-sized pot and cover with water. Bring to a low boil for 25-30 minutes or until the beet is soft. Drain the excess water and allow the beet to cool before using a blender to puree. Add 1 tbsp of water if needed. Scoop out 2 tbsp of the beet puree to use in the cookies. See notes for leftovers.
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Line a baking sheet with lightly greased parchment paper and preheat the oven to 350 F.
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Using a medium-sized bowl, mix the coconut flour, arrowroot, cocoa powder, and baking soda until well combined.
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Mix in the beet puree, palm shortening, and maple syrup. Stir until the dough is fully combined.
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Scoop 1 tbsp of the cookie dough onto the baking sheet and use the palm of your hand to flatten into a cookie. Repeat the process for the rest of the dough. You should have about 12 cookies.
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Bake in the preheated oven for 10 minutes. Carefully move to a cooling rack and allow to cool. These cookies will easily break if not cooled.
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Prepare the cream filling by whisking together the shortening and sweetener.
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Once the cookies have cooled, add a spoonful of cream filling to the bottom of a cookie and sandwich it with another cookie. Repeat for 6 whoopie pies total.
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Chill in the refrigerator to set the frosting before serving (preferred) or eat immediately for a smoother frosting.
Notes
All nutrition facts are estimations and will vary.
For the cream filling, the honey yields a better color for the cream. However, you can also use maple syrup if you’re sharing with vegan friends.

More Delightful & Healthy Dessert Inspirations
If you’ve enjoyed these Red Velvet Whoopie Pies, you might also love exploring other delicious and health-conscious recipes from my kitchen. Here are a couple of favorites that align with similar dietary principles and offer equally satisfying flavors:
- No-Bake Cake Pops (Paleo): For a quick and easy treat that requires no oven time, these cake pops are fantastic. They offer a bite-sized indulgence that’s rich in flavor and healthy ingredients.
- Paleo Brownie Skillet: Craving something warm, gooey, and deeply chocolatey? This brownie skillet is perfect for sharing (or not!). It’s a comforting dessert that’s surprisingly simple to make and completely paleo-friendly.
Conclusion: Indulge Without Compromise
These Red Velvet Whoopie Pies are more than just a dessert; they are a testament to the fact that healthy eating doesn’t mean sacrificing flavor or fun. With their naturally vibrant color, soft cookie texture, and creamy filling, they offer a truly satisfying experience while adhering to Paleo, Gluten-Free, Dairy-Free, and AIP dietary guidelines. They’re perfect for celebrating special moments or simply treating yourself to a wholesome, delicious snack. So go ahead, gather your ingredients, follow these simple steps, and create a batch of whoopie pies that will bring joy to your taste buds and peace of mind to your dietary journey. Happy baking!