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These gluten-free vegan peanut butter cup cupcakes are rich, decadent, and topped with creamy frosting, making them a perfect treat for any sweet tooth.

This recipe makes 12 chocolate peanut butter cup cupcakes.

Table of Contents

(click the links below to skip to the section you’re looking for)

• Chocolate Cupcake Recipe
• Peanut Butter Filling Recipe
• Chocolate Frosting Recipe
• Frequently Asked Questions
• Ingredient Substitutions
• Video
• Nutritional Information
• Contact Me with Questions
• Similar Recipes

I originally wrote this recipe in 2014. I made them for Kimmy’s birthday back when she avoided gluten. Now, in 2025, our friend Sarah was diagnosed with celiac disease, so I’m making them again for her birthday.

The recipe is perfect, so I’m not changing a thing. I am updating the pictures and adding more details since I used to write for the experienced baker, and now I try to write for everyone.

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Ingredients for the Gluten-free Chocolate Cupcakes Recipe

(jump to the substitutions section to see ingredient details and suggestions for substitutions)

• 1 cup (240g) soymilk
• 1 tablespoon (15g) apple cider vinegar
• ⅓ cup (80g) coconut oil
• 1 cup (192g) coconut sugar
• 1 tablespoon (15g) vanilla extract
• ¼ cup (30g) tapioca flour
• 2 tablespoons (16g) ground flax seeds
• ¼ cup (28g) almond flour
• ½ cup (80g) rice flour
• ¼ cup (28g) quinoa flour
• ¼ cup (30g) fava-chickpea flour
• ½ cup (48g) cocoa powder
• 1 ½ teaspoons (6g) baking powder
• ¾ teaspoon (4g) baking soda

How to Make Vegan Gluten-free Chocolate Cupcakes

prep time: 20 min | bake time: 22 min

Preheat the Oven. Turn on the oven to 350°F (175°C).

Prepare Pans. Get out 2 cupcake pans, and add cupcake papers to 15 cubbies. If you only have one cupcake pan, buy another one. Just kidding. If you only have one, get out 3 oven-safe ramekins and put paper liners in them.

Mix Wet Ingredients. Mix all the wet ingredients together. They include: 1 cup (240g) soymilk, 1 tablespoon (15g) apple cider vinegar, ⅓ cup (80g) coconut oil, 1 cup (192g) coconut sugar, and 1 tablespoon (12g) vanilla extract.

Combine Dry Ingredients. Sift the dry ingredients into a separate bowl. They are ¼ cup (30g) tapioca flour, 2 tablespoons (16g) ground flax seeds, ¼ cup (28g) almond flour, ½ cup (80g) rice flour, ¼ cup (28g) quinoa flour, ¼ cup (30g) fava-chickpea flour, ½ cup (48g) cocoa powder, 1 ½ teaspoons (6g) baking powder, and ¾ teaspoon (4g) baking soda. Whisk the dry ingredients until it all looks one color.

Before the next step, make sure the oven is preheated (or is only 10 degrees away from being at the desired temp). This is important because the moment the wet ingredients touch the dry ingredients, the magic starts to happen. You want that magic happening in the oven and not on your kitchen counter.

Combine Dry and Wet Ingredients. Add the dry ingredients to the wet ingredients. Mix with a baking spatula. Make sure you scrape the bottom and sides to dislodge any dry ingredients that might be hiding. As soon as you no longer see dry ingredients, stop mixing.

Fill Cupcake Pans. Fill the cupcake papers about 80% full. I use my number 16 (4 tablespoon) scoop for this step. This recipe should make around 15 cupcakes. If you’re like me, that means you’re taking 12 cupcakes to the party, and keeping 3 for yourself (oink oink 🐷).

Bake Cupcakes. Bake the cupcakes on the same rack of the oven for an even bake. Bake at 350°F (175°C) for around 20-24 minutes. Baking times vary because all ovens are a little different. Insert a toothpick into the center of a couple. If it comes out clean, they’re ready. If it doesn’t, bake them for a few minutes, and test them again.

Cool Cupcakes. Once the cupcakes pass the toothpick test, take them out of the oven and leave the pans on cooling racks to cool completely.

Ingredients for Gluten-free Peanut Butter Filling Recipe

(jump to the substitutions section to see ingredient details and suggestions for substitutions)

• ½ cup (88g) vegan butter or margarine
• ½ cup (100g) spectrum palm shortening
• ½ cup (128g) peanut butter
• 2 tablespoons (42g) blackstrap molasses
• 1 tablespoon (15g) vanilla extract
• 2 cups (240g) organic powdered sugar
• 1 cup (96g) peanut butter powder
• ⅛ cup non-dairy milk (only if needed)

How to Make Vegan Peanut Butter Filling

prep time: 18 min

Mix Wet Ingredients. Use a stand mixer fitted with a whisk or paddle attachment to mix the wet ingredients. They are ½ cup vegan butter, ½ cup spectrum palm shortening, ½ cup peanut butter, 2 tablespoons molasses, and 1 tablespoon vanilla extract. If you don’t have a stand mixer, use a handheld electric mixer. You can probably do it by hand if you have patience and upper body strength. But I have neither, so I’ve never tried. Once these ingredients are fluffy, move on to the next step.

Add Dry Ingredients. Sift 2 cups of organic powdered sugar into the wet ingredients, half at a time, mixing after each addition. Add 1 cup of peanut butter powder next. If it’s not lumpy, you may not have to sift it, but if has even the tiniest lump, I recommend sifting this ingredient too. If the filling is getting too thick and not looking creamy, add nondairy milk, a teaspoon at a time (so you don’t accidentally add too much).

Fill Cupcakes. Fill the cooled cupcakes with this peanut butter filling filling you just made. There are 2 ways to do this. One way is to fill a piping bag with the filling and poke the tip into the top of the cupcakes and squeeze in as much as you can. Another way is to use the method I used for my strawberry filled cupcakes.

Transfer Remainder to Piping Bag. Transfer any leftover filling to a disposable piping bag for later, if it’s not already in one.

Ingredients for Chocolate Peanut Butter Frosting Recipe

(jump to the substitutions section to see ingredient details and suggestions for substitutions)

• ¼ cup (44g) vegan butter or margarine
• ¼ cup (50g) vegan shortening
• 1 teaspoon (4g) vanilla extract
• 1 ½ cups (180g) organic powdered sugar
• ¼ cup (24g) cocoa powder

How to Make Vegan Chocolate Peanut Butter Frosting and Decorate the Peanut Butter Cup Cupcakes

prep time: 20 min

Mix Wet Ingredients. Use a stand mixer or handheld electic mixer to mix the wet ingredients. They are ¼ cup (44g) vegan butter, ¼ cup (50g) vegan shortening, and 1 teaspoon (4g) vanilla extract. Stop the mixer to scrape the sides and bottom of the mixing bowl with a silicone spatula and mix again. Stop mixing once the consistency has changed to super fluffy.

Sift Dry Ingredients. While the stand mixer is busy mixing the stand mixer and vegan butter, sift the dry ingredients. They are 1 ½ cups (180g) organic powdered sugar and ¼ cup cocoa powder.

Add Dry Ingredients to Wet Ingredients. One cup at a time, add the sifted dry ingredients to the mixing bowl, and mix after each addition. If at any time, it starts to get too thick, add a teaspoon of nondairy milk or vegan creamer. You want to be able to pipe it, but you also want it stiff enough to keep it’s shape.

Transfer to Piping Bag. Transfer this chocolate frosting to a disposable piping bag. If you have a lot of reusable piping bags, you can use those instead. It takes 12 minutes to make the chocolate frosting and fill the piping bag with it.

Frost Cupcakes. To frost your chocolate peanut butter cup cupcakes, place both of the piping bags you filled into another piping bag fitted with your favorite tip. My favorite tip is the Wilton 1M open star tip. Make sure when you put the chocolate frosting piping bag and the peanut butter filling piping bag into the larger piping bag, you set them side by side as much as possible. If you’re a perfectionist, practice on a plate before starting to frost the cupcakes. It takes me 5 minutes to frost all the cupcakes.

Garnish Cupcakes. To make your peanut butter cup cupcakes extra special, drizzle with chocolate sauce and or bite-sized peanut butter cups.

Ingredient Details and Substitutions

• Soymilk: I’ve used soymilk, coconut-almond milk, and oat milk to make these and they all work fine. If you want them to be gluten-free, make sure the nondairy milk you use is gluten-free. The ⅛ cup non-dairy milk for the peanut butter filling is optional. You only use it if the consistency is getting thick. I used it in both my peanut butter filling, as well as my chocolate frosting.
• Apple Cider Vinegar: You can replace the apple cider vinegar an equal amount of with lemon juice, lime juice, or white vinegar. You just need some sort of acid to interact with the alkalinity of the baking soda to make the cupcakes rise.
• Coconut Oil: I recommend using safflower, sunflower, avocado oil, or coconut oil for baking cupcakes because those oils are made for high heat. However, you can use any other oil such as vegetable oil, canola oil, grapeseed oil, etc. People even use olive oil, but I don’t recommend it.
• Coconut Sugar: For the sugar in this recipe, you can use any number of sugars, as long as they’re vegan: sucanat, coconut sugar, raw sugar, or organic sugar. If you’re not sure if your sugar is vegan, you can contact the company and ask, but basically, just avoid conventional white sugar or granulated sugar, and you should be ok.
• Vanilla Extract: You can sub vanilla powder, instead of extract. Use an equal amount of the powder, but add it when you add dry ingredients.
• Gluten-Free Flours: This recipe calls for a wide variety of flour. If you don’t normally have this stuff in your house, just replace the tapioca flour, almond flour, rice flour, quinoa flour, and fava-chickpea flour with 1 ½ cups of all-purpose gluten-free flour. Bob’s Red Mill makes a good one.
• Ground Flax: If you don’t have ground flax, but you have flax seeds, you can just put 2 tablespoons (16g) of flax seeds in a coffee or spice grinder or a coffee grinder. I would just sift it after to make sure you don’t have any whole seeds in your cupcakes.
• Cocoa Powder: I use organic and fair trade cocoa powder but you can use any kind you have. Just make sure it’s natural cocoa powder, because if it’s dutch processed, you’ll need to reduce the amount of baking soda you use.
• Baking Powder: You can replace the 1 ½ teaspoons (6g) baking powder in this recipe with and additional ½ teaspoon (2-3g) baking soda.
• Baking Soda: You can replace the ¾ teaspoon (4g) baking soda in this recipe with and additional 1 ½ teaspoons (6g) baking powder.
• Vegan Butter: If you’re out of vegan butter, replace it with additional shortening. I like to buy the organic whipped Earth Balance. If you avoid soy, get the soy-free earth balance.
• Vegan Shortening: I buy Spectrum sustainable organic palm shortening but you can use any vegan shortening you have.
• Peanut Butter: I use a variety of peanut butters. Costco has a 2 pack of organic creamy peanut butter for a good price. You can use this link to get 10% off any Peanut Butter & Co peanut butter. Or you can replace the peanut butter with almond or cashew butter. If you are making this for someone with a nut allergy, try replacing the peanut butter with sunflower seed butter.
• Molasses: The 2 tablespoons (42g) blackstrap molasses in this recipe is optional.
• Powdered Sugar: Try to find organic powdered sugar to make sure that it’s vegan. Read more about which powdered sugar brands are vegan here.
• Peanut Butter Powder: If you can’t find peanut butter powder for the filling recipe, you can replace it with another cup of powdered sugar.

Nutrition Facts

When calculating this information, I assume that one peanut butter chocolate cupcake is a serving. This info is just for the cupcake, filling and frosting. Garnishes are not included.

• Servings: 12
• Calories per serving: 602
• Calcium per serving: 118mg
• Cholesterol per serving: 0mg
• Dietary Fiber per serving: 5g
• Iron per serving: 2mg
• Potassium per serving: 306mg
• Protein per serving: 10g
• Total Carbohydrate per serving: 66g
• Total Fat per serving: 33g
• Total Sugars per serving: 47g
• Sodium per serving: 275mg
• Vitamin A per serving: 75mcg
• Vitamin E per serving: 2mg

Comments or Questions?

If you make this gluten-free vegan cupcakes recipe, I would love it if you’d snap a pic, post to instagram, and tag me @vegandollhouse. It seriously makes my day/week/month!

Please message me (instagram or email) if you have any questions or feedback about the recipe.

Similar Recipes

If you like peanut butter and chocolate together and you’re not gluten-free, check out my vegan chocolate peanut butter cupcakes, my peanut butter chocolate pretzels, and my peanut butter chocolate cake.

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I use mostly organic ingredients when I cook, but I realize that not everyone has the disposable income to purchase all organic ingredients. Therefore, I only specify organic on the ingredients that really matter to ensure that the item is vegan.

This post links to items I mention. If you click on one, you will go to a website where you can buy the product. Sometimes, the store you purchase from will pay me for referring you. This costs you nothing extra, and I would never recommend a product that I don’t use. These affiliate programs help me buy ingredients to create recipes for you. Read more about this in my privacy policy.

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