Gluten-Free Vegan Peanut Butter and Jelly Thumbprint Cookies

Gluten free vegan peanut butter and jelly thumbprint cookies. Soft peanut butter cookies, filled with your favorite berry jam. The classic combo in a cookie!Gluten-free, vegan peanut butter and jelly thumbprint cookies — soft, tender peanut butter cookies with a sweet dollop of your favorite berry jam. The familiar sandwich combination, reimagined as a comforting cookie.

I still love a classic peanut butter and jelly sandwich. The contrast of salty, creamy peanut butter with bright, fruity jam is simple and satisfying, and for many it carries warm, nostalgic memories. These thumbprint cookies capture that same comforting flavor in a bite-sized treat that’s naturally portable and hard to resist.

I’d been meaning to make gluten-free, vegan PB&J thumbprint cookies for months. When I finally made them, they exceeded expectations: soft and slightly chewy peanut butter cookies with a glossy jam center that stays soft after baking. They went quickly in my household — everyone loved them, and I certainly had more than my fair share.

The dough comes together easily with pantry-friendly ingredients. The cookies hold their shape, develop a gentle crackle on the surface, and the jam remains bright and flavorful. These are perfect for lunchboxes, potlucks, or a weekend baking session when you want an uncomplicated, nostalgic treat.

Gluten free vegan peanut butter and jelly thumbprint cookies. Soft peanut butter cookies, filled with your favorite berry jam. The classic combo in a cookie!

Gluten Free Vegan Peanut Butter and Jelly Thumbprint Cookies
Recipe Type: Cookies
Author: Sarah Bakes Gluten Free
Serves: 28–30
Ingredients
  • 2 cups plus 3 tablespoons Sarah’s gluten-free flour blend
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon sea salt
  • 1 cup packed brown sugar
  • 1/2 cup creamy peanut butter
  • 1/4 cup refined coconut oil, melted
  • 1/4 cup unsweetened almond milk or coconut milk, room temperature
  • 3 tablespoons pure maple syrup, room temperature
  • 1 teaspoon pure vanilla extract
  • 1/2 cup strawberry or raspberry jam
Instructions
  1. Preheat the oven to 350°F (175°C). Line baking sheets with parchment paper.
  2. In a medium bowl, whisk together the gluten-free flour blend, baking powder, baking soda, and sea salt. Set aside.
  3. In a large bowl, cream the brown sugar, peanut butter, and melted coconut oil until smooth and combined.
  4. Add the almond or coconut milk, maple syrup, and vanilla extract to the peanut butter mixture. Mix until fully incorporated. Stir in the dry ingredients until a soft dough forms.
  5. Scoop heaping tablespoon-sized portions of dough and roll into balls. Place the balls on the prepared baking sheets, spacing them about 2 inches apart. Use your thumb or the back of a teaspoon to gently press an indentation in the center of each cookie.
  6. Bake the cookies for 5–6 minutes, then remove the baking sheet from the oven. Carefully fill each indentation with about 1/2 teaspoon of jam. Return the cookies to the oven and bake an additional 5–6 minutes, until the cookies are set and lightly golden at the edges.
  7. Allow the cookies to cool on the baking sheet for 3–4 minutes, then transfer them to a cooling rack to cool completely. The jam will set as the cookies cool, but remain soft and glossy.
Tips and Variations
  • For a thicker jam center, gently press a slightly deeper indentation before baking or add a bit more jam after the first short bake.
  • Substitute sunflower seed butter for peanut butter to make these nut-free (note: color and flavor will differ slightly).
  • Use your favorite jam—strawberry and raspberry work beautifully. Seedless preserves give a smoother finish.
  • Chill the dough briefly if it becomes too soft to shape comfortably, especially in warm kitchens.
  • Store cooled cookies in an airtight container at room temperature for up to 3 days, or freeze for longer storage.