Gluten Free Peanut Butter and Jelly Cupcakes
Combine the classic PBJ with every kid’s favorite dessert to make these super fun Gluten Free Peanut Butter and Jelly Cupcakes. Moist and tender vanilla cupcakes are stuffed with PB&J, then topped with fluffy peanut butter frosting and a dollop of jelly. Perfect for a party, but easy enough to enjoy any day you want a sweet treat!

Delicious Details
- Cuisine Inspiration: American
- Primary Cooking Method: Oven
- Dietary Info: Gluten-free
- Skill Level: Easy
Whether you are a kid or a kid at heart, the sweet and salty pairing of peanut butter and jelly will transport you to childhood. I love taking those nostalgic flavors and transforming them into a new treat, whether it’s a Peanut Butter and Jelly Yogurt Parfait for breakfast, a Peanut Butter and Jelly Smoothie as a snack, or Peanut Butter and Jelly White Chocolate Bark as a sweet treat.
So naturally, I couldn’t resist turning everyone’s favorite sandwich into a cupcake. These Peanut Butter and Jelly Cupcakes start with my basic Gluten Free Vanilla Cupcakes, but a double dose of PB&J turn then into a treat that is sure to delight everyone. They are perfect for a birthday, great to take to a potluck, or a fun treat to celebrate the first day of school, or even the last!
Peanut Butter and Jelly Cupcakes are Stuffed with Nostalgia!
So simple to make, despite being totally epic with the level of peanut butter goodness and the right amount of sweet fruity jelly, here’s why you’ll love them…
- So much PB&J flavor. They are filled with pure peanut butter and jelly. Not a peanut butter custard or cream or buttercream. Actual peanut butter. So you get that nutty, salty flavor that goes amazingly well with the sweetness of those cupcakes.
- Dreamy frosting. This isn’t a buttercream with a little peanut butter flavor. It’s truly a peanut butter frosting with just enough butter to make it creamy and smooth. Be sure to whip it for a bit to make it light and fluffy.
- Finished off just right. Then it all comes together with a dollop of jelly on top. Seriously, it’s definitely peanut butter jelly time!

Recipe Ingredients
Here’s a rundown of what you need to make these fun and fabulous cupcakes. Plus, I share a little extra info you might need so you can bake them up just right, and a few extra tips below so they turn out perfectly. Scroll down to the recipe card for the full amounts and step-by-step instructions.
For the cupcakes
- Greek yogurt: You’ll need plain Greek yogurt to give these cupcakes their perfect texture.
- Vegetable oil: If you like you can substitute cooled melted butter or another neutral-flavored oil.
- Vanilla: Pure vanilla extract gives the best flavor.
- Egg: Let it warm to room temperature for the best results.
- Milk: I use whole milk, but a low fat or non-dairy milk can be used, though it will affect the final texture a bit.
- 1:1 Gluten Free Flour: Be sure to use a 1-to-1 baking blend with xanthan gum.
- Sugar: Just regular white granulated sugar.
- Baking Powder: So your cupcakes rise perfectly.
- Salt: Just a little to enhance the sweet flavors
For the frosting and filling
- Peanut butter: Creamy works best, but you can use your favorite brand. You’ll need some to stuff in the cupcakes and more for the frosting.
- Unsalted butter: Let it soften to room temperature.
- Powdered sugar: For perfectly sweet (but not too sweet) peanut butter frosting.
- Vanilla: Makes the flavors pop.
- Jelly: Strawberry, grape, or whatever flavor you love. Again, you’ll need some to fill the cupcakes and more to dollop on top.


How to Make Peanut Butter and Jelly Cupcakes
There are a few different steps, but overall it’s really quite simple to make these stuffed cupcakes. All of the details are broken down in the recipe card at the bottom of the post, but here is a little overview.
- Make the cupcakes: Preheat the oven to 350°F and line a pan with cupcake liners. Whisk together the wet ingredients, then add the dry ingredients and whisk until just combined. Rest, bake, and cool the cupcakes.
- Make the frosting: Beat the butter, then blend in the peanut butter until combined. Add the powdered sugar and vanilla extract, and beat until light and fluffy.


- Fill the cupcakes: Once cupcakes are completely cooled, spoon peanut butter and jelly into a pastry bag that has been fitting with a small round tip. Insert tip into the center of the cupcake and squeeze to fill the cupcakes. Remove the tip and repeat with all of the cupcakes.

- Frost and enjoy: Pipe or spread the peanut butter frosting on top of the filled cupcakes and leave a little indentation that you can fill with a dollop of jelly. Then get ready to sink your teeth into these peanut butter and jelly cupcakes.


Tips for Success
- Let the batter rest: These cupcakes turn out perfectly when you give the batter about 20 minutes so the gluten free flour can absorb the liquid to create the right consistency.
- Or use a cake mix: You can also keep it super simple by using your favorite gluten free cake mix and follow the directions to make cupcakes. If your mix makes 12 cupcakes, then follow along with the recipe. If it makes 24, you’ll need to double the frosting.
- Cool completely: You don’t want the filling to melt and absorb into the cupcakes or the frosting to run off the top.
- Have the right supplies: While you can just use a knife or small offset spatula to frost the cupcakes, it is helpful to have pastry bags and decorating tips to fill the cupcakes. A round #4 tip is perfect for stuffing the peanut butter and jelly cupcakes, and a #2A tip will give you a nice swirl on top.
- Storing cupcakes: These cupcakes can be kept in a covered container for 3 to 4 days. Any container will do, but I do love a cupcake carrier if I have to transport them anywhere.

More Gluten Free Cupcakes
Cupcakes are always a hit! Here are a few of my favorites…

Gluten Free Peanut Butter and Jelly Cupcakes
Ingredients
For the cupcakes:
- 1/2 cup whole milk
- 1/2 cup plain Greek yogurt
- 1/4 cup vegetable oil
- 1 egg, at room temperature
- 2 teaspoons vanilla extract
- 1 1/3 cup gluten-free 1:1 baking flour
- 1 cup granulated sugar
- 1 1/2 teaspoons baking powder
- 1/2 teaspoon salt
- 1/4 cup creamy peanut butter
- 3 Tablespoons jelly + 2 Tablespoons, divided (any flavor)
For the frosting:
- 1 1/2 Tablespoons unsalted butter
- 1/2 cup creamy peanut butter
- 1/2 cup powdered sugar
- 1/4 teaspoon vanilla extract
Instructions
For the cupcakes:
- Preheat oven to 350°F and line a 12-well cupcake pan with cupcake liners.
- In a mixing bowl, whisk together 1/2 cup plain Greek yogurt, 1/2 cup plain Greek yogurt, 1/4 cup vegetable oil, 1 egg, and 2 teaspoons vanilla extract.
- Add 1 1/3 cup gluten-free 1:1 baking flour, 1 cup granulated sugar, 1 1/2 teaspoons baking powder, and 1/2 teaspoon salt. Whisk together until just combined.
- Cover the mixing bowl with plastic wrap and allow to sit for 20 minutes. This allows the gluten-free flour time to absorb more liquid.
- Once the batter is ready, fill each cupcake liner 2/3 of the way full.
- Bake at 350°F for 15 – 20 minutes, or until cooked through. A toothpick should come out clean when inserted into the center of the cupcake.
- Allow the cupcakes to cool for 5 minutes in the pan, and then transfer to a cooling rack to cool completely. While they are cooling, prepare the frosting.
- Once cupcakes are completely cooled, spoon the 1/4 cup creamy peanut butter and 3 Tablespoons jelly into a pastry bag using a smaller round tip like the Wilton #4. Insert tip into the center of the cupcake and fill with the peanut butter and jelly mixture. Once filled, remove the tip from the cupcake. Set aside and continue filling remaining cupcakes.
- Spoon the frosting into a pastry bag with a round tip such as the Wilton #2A to pipe with a onto cupcakes or frost with a knife.
- Use a knife or small spatula to make a small indentation in the top of the frosting and spoon a teaspoon of jelly onto the tops of the cupcakes. Enjoy.
For the frosting:
- Add 1 1/2 Tablespoons unsalted butter to a mixing bowl or the bowl of a stand mixer. Using a hand mixer or the whisk attachment on your stand mixer, beat the butter at medium speed for about 1 minute, until it is creamy. Add 1/2 cup creamy peanut butter and continue to beat on medium speed until completely combined with the butter. It will be nice and creamy
- Add 1/2 cup powdered sugar and 1/4 teaspoon vanilla extract. Mix over medium speed until completely combined. Then increase the speed to high and beat until the frosting is light and fluffy. Set aside until ready to use, or cover and store in the refrigerator overnight.




