Gluten-Free Peanut Butter and Jelly Thumbprint Cookies

These Peanut Butter Jelly Cookies capture the best of a classic PB&J in soft, chewy, gluten-free thumbprint cookies. The dough blends creamy peanut butter with a mix of oat and almond flours for a rich, nutty base, while a spoonful of strawberry jam in the center delivers the familiar sweet-tart finish. This recipe focuses on simple, natural ingredients and straightforward techniques so bakers of any skill level can make an impressive batch. Use my naturally sweetened homemade strawberry jam or your favorite store-bought variety.

They’re ideal for holiday cookie exchanges, lunchboxes, or whenever you want the comforting flavors of a peanut butter and jelly sandwich in cookie form.

Why You’ll Love This Gluten-Free Peanut Butter and Jelly Cookie Recipe

• Made with Simple Ingredients: Most items are pantry staples.
• Reliable Texture: Soft and chewy with a slight crunch from the nut coating.
• Family-Friendly: Kid-approved and perfect for all ages.
• Customizable: Swap jams or nut butters to create new flavor combinations.

Ingredients & Substitutions

Everything you need to make these gluten-free PB&J thumbprint cookies:

Almond Flour: Can be replaced with cashew flour or sunflower seed flour.

Oat Flour: Use store-bought oat flour or grind oats into flour.

Tapioca Flour: Adds chewiness and structure. Substitute arrowroot or cornstarch, or use a gluten-free flour blend.

Alternative flour combinations (equivalent to the recipe card):

Creamy Peanut Butter: Swap for crunchy peanut butter, almond butter, sunflower seed butter, or tahini.

Butter: Use coconut oil or plant-based butter for dairy-free cookies.

Sugar: Cane sugar works well; coconut sugar, brown sugar, or granulated white sugar are valid substitutes.

Vanilla Extract: Optional; 1/2 teaspoon almond extract is a nice alternative.

Apple Cider Vinegar: White vinegar or lemon juice will also help with texture.

Egg White: Replace with a flax or chia egg for an egg-free version.

Baking Soda & Baking Powder: Use the stated amounts and ensure they are fresh.

Jam: Strawberry is classic here, but raspberry, apricot, or grape work too.

Chopped Peanuts: Replace with chopped almonds, cashews, pecans, seeds, or omit the coating entirely.

How to Make My Peanut Butter and Jelly Thumbprint Cookies

Below are clear, step-by-step instructions. The same directions are included in the recipe card at the end of this post.

Step 1: Make the Strawberry Jam (optional)

You can make a simple, naturally sweetened strawberry jam or use a favorite store-bought jam.

Step 2: Make the Peanut Butter Cookie Dough

Preheat the oven to 350°F (175°C) and line a baking sheet with parchment paper.

In a mixing bowl, cream together 1/4 cup peanut butter, 1/4 cup butter, 2/3 cup cane sugar, 2 teaspoons vanilla extract, and 1 teaspoon apple cider vinegar. Add 1 egg white and mix until just combined.

Stir in 1 cup almond flour, 1 cup oat flour, 1/4 cup tapioca flour, 1/2 teaspoon baking soda, 1/4 teaspoon baking powder, and 1/2 teaspoon salt. Mix until a soft cookie dough forms. The dough should be soft but not sticky; add a little extra flour if needed.

Step 3: Form the Cookies

Roughly chop 1/2 cup peanuts into 1/8″ pieces (not a powder) and place in a shallow bowl.

Use a tablespoon or small cookie scoop to portion the dough. Roll each portion into a smooth ball, coat it in the crushed peanuts, and arrange on the prepared baking sheet. Press a thumb or the back of a spoon into the center to create a well about 1/4″ thick on the sides. Fill each well with about 1 teaspoon of strawberry jam.

Bake 11–13 minutes, until the edges are golden. Cool completely on a wire rack before serving.

Optional garnish: Sprinkle chopped peanuts and a tiny pinch of coarse sea salt on each cookie.

Expert Recipe Tips

Chill if Too Soft: If the dough is hard to handle but not sticky, chill it in the fridge or freezer for a few minutes.

Roll Smoothly: Smooth dough balls reduce cracking during baking.

Delicious Serving Suggestions

• Snack Time: Great with a cold glass of milk.
• Lunchbox Treat: Add one to a lunchbox for a sweet surprise.
• Dessert Table: Lovely on a cookie tray at parties or holidays.
• Gifts: Pack in a tin for a homemade present.
• Breakfast: Serve with yogurt or fresh fruit for a playful morning treat.
• Picnic or Movie Night: Easy to transport and share.