Gluten-Free Peanut Butter Cup Cookies

These gluten-free peanut butter cup cookies are stuffed with mini Reese’s peanut butter cups and topped with a few M&Ms for a cookie that is rich, chewy and crunchy. They’re perfect for birthday parties, Christmas cookie swaps, or a fun baking day with the family.
Chocolate chip cookie cup with a mini peanut butter cup inserted into the center and topped with three M&Ms.
Multiple peanut butter cup cookies with M&Ms on a round wire cooling rack.

These gluten-free peanut butter cup cookies are a unique twist on a classic treat.  Smooth peanut butter cups and crunchy M&Ms are nestled in a chewy gluten-free chocolate chip cookie cup for a cookie that has such a satisfying texture and flavor! 

They’re easy to make and perfect for sharing. Whether for a special occasion or a casual treat, these cookies are sure to be a hit with everyone.

Growing up, my mom made these cookies with store-bought cookie dough that we would break and place in each muffin well. Since I was diagnosed with celiac disease over 10 years ago, I thought these cookies were part of my past.

I’ve made them in recent years with gluten-free store-bought cookie dough since it is more readily available, but it can easily get expensive since those products tend to cost a premium at grocery stores. Finally, I’m sharing this recipe to make your peanut butter cup cookies from scratch! The dough is ready in under 10 minutes, making it just as easy as buying that store-bought cookie dough!

You’ll love this recipe because:

  • Simple and fun to make. This recipe is straightforward and easy to prepare, making it a perfect baking project for both beginners and experienced bakers, as well as a fun activity to do with kids. They’ll love pressing the mini peanut butter cups down into the freshly baked cookies!
  • Perfect for any occasion. These cookies are not only great for everyday treats but also make an impressive addition to parties, holiday gatherings, or as special homemade gifts. Use specific colors of M&Ms to personalize these cookie cups for your party! 
  • Quick to prepare. I love this recipe because you can make so many cookies at one time! Mini muffin tins normally come with either 12 or 24 muffin wells, and this recipe makes 18 mini cookie cups. You can pop 1-2 trays into the oven all at the same time – no need to bake the cookies in batches! Plus, the dough is ready in just about 10 minutes, so this is a quick baking project that the whole family will love doing together.
  • They’re gluten-free! Using a gluten-free flour blend, like Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour makes it very simple to make these cookies gluten-free for those with celiac disease or gluten intolerances. Plus, did you know that regular M&Ms and Reese’s mini peanut butter cups don’t contain gluten?

Ingredients

Ingredients in small bowls to make gluten-free peanut butter cup cookies with M&Ms, including mini peanut butter cups, vanilla extract, butter, chocolate chips, baking soda, brown sugar, egg, salt, granulated sugar, M&Ms and gluten-free flour with text overlays over each ingredient.

Ingredient Notes

  • Gluten-Free Flour Blend – I’ve tested this recipe using Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour found in the blue bag. This blend is specially formulated to mimic the texture and baking properties of wheat flour. It already contains xanthan gum, so you will not need to add it to your recipe. 
  • Baking Soda – Ensure your baking soda is fresh for optimal rise, as it loses potency over time.
  • Salt – I used table salt for this recipe but you can also use sea salt. 
  • Unsalted Butter – Make sure your unsalted butter is at room temperature so it creams together with the sugar easily. I also like to use unsalted butter to ensure I have control over the salt content in the recipe. 
  • Brown Sugar – Adds moisture and a rich, caramel-like flavor. Light brown sugar is what I use, but dark brown can be substituted for a deeper molasses flavor.
  • Granulated Sugar – I like to use a blend of brown sugar and white sugar in my chocolate chip cookies for optimal flavor, browning and sweetness. 
  • Egg – Ensure your egg is at room temperature for better incorporation. I use large eggs which are 50 grams.
  • Vanilla Extract – Pure extract is preferable, but imitation vanilla can be used. Just ensure it’s gluten-free if needed.
  • Mini Chocolate Chips – I prefer to use mini chocolate chips when I’m making these cookie cups because regular chocolate chips or chunks seem to throw off the ratio of cookie dough to chocolate. Plus, when you press a peanut butter cup into the center of the cookie, there isn’t a lot of room for the chocolate chips. 
  • Mini Peanut Butter Cups – I use Reese’s mini peanut butter cups for this recipe, which are labeled gluten-free. Always be sure to double check your bag to ensure it’s gluten-free, as I’ve heard that sometimes the holiday ones are not gluten-free. 
  • M&Ms – Add a crunchy texture and color to the top of these cookie cups. Use regular M&Ms, which are gluten-free. If you’re making these for a specific holiday use coordinating colors. For example, for Christmas, use red and green M&MS.

Timing is key with this recipe. You’ll want to add the Reese’s peanut butter cups to the cookie cups when the cookies come out of the oven so they are still warm. This will allow you to press the peanut butter cup down into the cookie easily. You’ll also want to wait until the chocolate has melted on the peanut butter cups in order to add the M&Ms to the top so they will stick to the cookies. 

Step-by-Step instructions

These Reese’s peanut butter cup cookies are very simple to make with mini peanut butter cups and M&Ms! The below photos are not meant to be the full recipe, but are there to help you see the recipe made at various stages so that you can make these gluten-free cookies perfectly every time!

For the ingredient list with measurements, full instructions, printable recipe, and additional notes, please scroll down to the recipe card.

A glass mixing bowl of gluten-free flour topped with baking soda and salt before whisking together.
In a medium bowl, add together the gluten-free flour blend, baking soda, and salt. Whisk to combine.
A glass mixing bowl with brown sugar, granulated sugar and a stick of softened butter.
In a separate large bowl, add the room temperature butter, brown sugar, and granulated sugar. Cream together until light and fluffy.
A glass mixing bowl of a creamed butter and brown sugar mixture next to a raw egg before mixing together.
Add the egg and vanilla extract. Mix until smooth.
A glass mixing bowl of gluten-free cookie dough mixture topped with gluten-free flour before mixing together.
Gradually add the dry ingredients to the wet mixture. Mix until just combined, until no more streaks of flour remain.
A glass mixing bowl of gluten-free cookie dough topped with a pile of mini chocolate chips before mixing together.
Add the mini chocolate chips to the cookie dough. Mix until evenly distributed.
A portion scoop of gluten-free chocolate chip cookie dough over a mixing bowl of additional cookie dough.
Use a cookie scoop to uniformly scoop the cookie dough into 18 balls. Place the cookie dough balls into a mini muffin tin lined with paper liners.
An overhead view of a mini muffin pan filed with chocolate chip cookie cups fresh out of the oven.
Bake the cookie cups in the oven until lightly browned. Do not overbake.
An overhead view of a mini muffin pan filed with chocolate chip cookie cups with mini peanut butter cups inserted in the center that have been melted.
Immediately press the mini peanut butter cups into the cookie cups. The chocolate will start to melt from the heat of the cookies.
An overhead view of a mini muffin tin filled with chocolate chip cookie cups with a mini peanut butter cup in the center topped with 3 M&Ms each.
Once the chocolate is melted, add a few M&Ms to the top of each cookie cup. Let the cookies cool completely before removing from the muffin pan.
Chocolate chip cookie cup with a mini peanut butter cup inserted into the center and topped with three M&Ms.
Serve and enjoy!

Recipe FAQs

What do I do if I don’t have any mini paper liners for the muffin wells?

You can generously grease the mini tin if you don’t have paper lines. Run a knife around each cookie cup after they have cooled to release it from the pan. 

What can I use instead of mini peanut butter cups?

If you don’t want to use a mini peanut butter cup, you can use other gluten-free candy’s such as a Snickers bar, a chocolate kiss, or a chunk of chocolate. You can also press the cookie down with a teaspoon to create a well and fill it with melted chocolate, buttercream, or whipped cream. 

Can I freeze the dough or the baked cookies?

Yes, both the dough and baked cookies freeze well. Bake the dough from frozen. Thaw cookies at room temperature for about an hour before serving.

Are M&Ms gluten-free?

Most M&Ms are generally considered gluten-free, making them suitable for a gluten-free diet. However, certain varieties, like Pretzel M&Ms, do contain gluten. Please also note that the crispy M&Ms use rice flour, however they also contain BARLEY MALT EXTRACT making them NOT gluten-free! As an alternative, you can use Sixlets, which are also colorful candy-coated chocolates and are labeled gluten-free, making them a safe and equally delightful option.

Are Reese’s peanut butter cups gluten-free?

Yes, the original Reese’s Peanut Butter Cups are gluten-free. This is indicated by a gluten-free label clearly displayed on the back of their packaging. However, it’s important to note that not all Reese’s products are gluten-free. Seasonal items, like Reese’s Eggs and Hearts, are not gluten-free due to cross-contamination during production. Always double check the package to ensure your Reese’s peanut butter cups are gluten-free if needed. 

How do I know when the cookies are done baking?

They should be lightly browned and puffed up but not hard. Overbaking will make them too crispy.

Can the recipe be doubled?

Yes, it can be easily doubled. Just ensure to maintain the ingredient proportions.

expert tips

  • Unwrap all of your mini peanut butter cups BEFORE the cookies are done baking. This will help ensure you are ready to insert the peanut butter cups as soon as the cookies come out of the oven. 
  • Use paper liners to line your mini muffin tin to ensure that your cookie cups are easy to remove from the pan. You can use decorated paper liners for holidays like Christmas to make your peanut butter cup cookies more festive!
  • Use a cookie scoop or measuring spoon to ensure your cookies are uniformly sized. This promotes even baking.
  • Wait for the peanut butter cups to melt from the heat of the baked cookies before adding the M&Ms. The melted chocolate will help the M&Ms adhere to the cookies.

Storage instructions

Storage

  • Room Temperature: Store the cookies in an airtight container at room temperature. They usually stay fresh for up to a week.

Freezer Directions

  • Freezing the Dough: You can freeze the cookie dough balls on a baking sheet, then transfer them to a freezer-safe bag or container. They can be stored for up to 3 months.
  • Freezing Baked Cookies: Once the cookies have cooled completely, place them in a freezer-safe container, separating layers with parchment paper. They can be stored for up to 3 months.

Reheat/Thaw:

  • Baking from Frozen: You can bake the dough straight from the freezer, but you may need to add a few extra minutes to the baking time.
  • Thawing Baked Cookies: Thaw them at room temperature for a few hours before serving.

Multiple peanut butter cup cookies with M&Ms on a round wire cooling rack with the front cookie cup cut in half to see the inside.

Did you make this recipe?

I’d love to know! Please rate it and leave a comment below. You can also share your pictures and tag @adashofmegnut on Instagram.

Chocolate chip cookie cup with a mini peanut butter cup inserted into the center and topped with three M&Ms.

Gluten-Free Peanut Butter Cup Cookies

These gluten-free peanut butter cup cookies are stuffed with mini Reese’s peanut butter cups and topped with a few M&Ms for a cookie that is rich, chewy and crunchy. They’re perfect for birthday parties, Christmas cookie swaps, or a fun baking day with the family.
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Course: Dessert
Cuisine: American
Diet: Gluten Free
Prep Time: 10 minutes
Cook Time: 12 minutes
Cooling Time: 30 minutes
Total Time: 52 minutes
Servings: 18 cookies
Calories: 180kcal
Author: Megan

Ingredients

  • 1 1/4 cups gluten-free flour blend (175g)
  • 1/2 tsp baking soda (3g)
  • 1/2 teaspoon salt (3g)
  • 6 tbsp unsalted butter (at room temperature (85g))
  • 1/2 cup brown sugar (100g)
  • 1/4 cup granulated sugar (50g)
  • 1 egg (50g, room temperature)
  • 1/2 tablespoon vanilla extract
  • 1/2 cup mini chocolate chips (80g)
  • 18 mini peanut butter cups
  • 1/3 cup M&Ms (65g)

Instructions

  • Preheat the oven to 350°F (175°C). Line a mini muffin pan with 18 mini paper cups. Set aside.
  • In a medium mixing bowl, combine gluten-free flour blend, baking soda and salt. Whisk to combine. Set aside.
  • In a large mixing bowl, add room temperature butter, brown sugar, and granulated sugar.
  • Cream with an electric mixer for 2-3 minutes, until light and fluffy, scraping down the sides of the bowl with a spatula as needed.
  • Add the egg and vanilla extract and mix until smooth.
  • Add half of the flour mixture to the butter mixture and stir until just combined. Repeat with the remaining flour, stirring until no more streaks of flour remain.
  • Stir in the mini chocolate chips.
  • Spoon the dough into each muffin well.
  • Bake at 350F for 10-12 minutes, until the cookies are puffed up and lightly browned. Do not overbake.
  • Remove from the oven and immediately press the mini peanut butter cups down into the cookies.
  • Once the chocolate on the mini peanut butter cups has melted from the heat of the cookies, add 3 M&Ms to the top of each cookie. Let the cookies cool completely before removing from the muffin wells.

Notes

  • If you have celiac disease or a gluten allergy, it’s crucial to double-check all ingredient labels and, if necessary, contact the manufacturer to confirm that the products are completely gluten-free. 
  • I tested this recipe with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour in the blue bag, which already contains xanthan gum. You do not need to add xanthan gum to this recipe. I cannot verify if other brands of gluten-free flour blends will work, as I have not tested them in this recipe. 
  • For best results, weigh your ingredients using a food scale. The way you measure floor can vastly change the recipe, so weighing it is the easiest way to ensure your recipe turns out perfectly every time. 
  • Keep an eye on the baking time; the cookies should be taken out when they are just set and lightly browned. They will continue to cook slightly once removed from the oven.

Nutrition

Calories: 180kcal | Carbohydrates: 25g | Protein: 2g | Fat: 9g | Saturated Fat: 5g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.2g | Cholesterol: 21mg | Sodium: 132mg | Potassium: 37mg | Fiber: 1g | Sugar: 18g | Vitamin A: 154IU | Vitamin C: 0.1mg | Calcium: 29mg | Iron: 1mg
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about megan

I’m Megan

A gluten-free food blogger from Chicago and lover of all things food, showing you gluten-free can be easy and delicious, too. Let’s make gluten-free stress free together! Read more…

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