Peanut Butter & Jelly Thumbprint Cookies

Peanut butter cookies… thumbprint cookies with jam centers… peanut butter and jelly sandwiches. Hmm. What if we combined each of these great things into an amazing peanut butter & jelly thumbprint cookie? (This is how I come up with recipe ideas…)

My favorite thing about these cookies is that they’re made with a full half cup of flaxseed, which is one of the healthiest foods on the planet. With their omega-3’s, lignans, antioxidants, and fiber, it’s no wonder that Dr. Greger recommends eating flax every day in his great new book, How Not to Die. The thing is, most recipes that call for flax use a frustratingly small amount (like a tablespoon across a dozen servings). But flax doesn’t have to be just a “seasoning” in your recipes; with a little maple syrup and some flour, it actually has a great flavor & texture in desserts like these cookies.

But don’t let all the nutrients and fiber and whole wheat and lack of refined sugar or oil scare you away – these cookies have an amazing soft texture with a mildly-sweet peanut butter flavor that works perfectly with the sweet jam centers.

You can use your favorite jam here (I used raspberry) or you can always make some of my homemade chia seed jam recipe for an even healthier option.



Makes 9-12 cookies


  • 1 cup whole wheat flour
  • 1/2 cup ground flaxseed
  • Pinch of salt
  • 1/2 cup peanut butter
  • 1/2 cup non-dairy milk
  • 1/2 teaspoon vanilla
  • 1/3 cup maple syrup
  • 1/4 cup jam

Step One

Preheat the oven to 350º F and set this Galantis song to play on repeat before continuing:

Step Two

In a large bowl, combine the dry ingredients: whole wheat flour, flaxseed, and a pinch of salt. Stir to combine. In a smaller bowl, combine all the wet ingredients, except for the jam: peanut butter, non-dairy milk, vanilla, and maple syrup. You may need to heat these wet ingredients until they are soft enough to be stirred into a smooth mixture.

Step Three

Pour the wet ingredients into the dry and gently mix until combined, doing your best not to overmix. Since there’s so much flax, which absorbs liquid, allow this to sit for 2-4 minutes and the batter will thicken slightly into the right texture for cookies. Then, roll into 9-12 even-sized balls and place on a greased baking sheet.

Step Three

Wet your fingers slightly so they don’t stick to the batter, then use your thumb (imagine that) to slightly flatten the cookie and make a little crater in the middle. Grab a spoon and your favorite jam (I used raspberry) and fill the crater with about 2 teaspoons of jam. Pop these in the oven and bake at 350º for 15-20 minutes (mine took 18), until the cookies are set and the jam is just starting to darken around the edges.

Caution: The jam centers will be molten-hot and very sticky, so handle them carefully when removing from the oven and allow to fully cool before serving.




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  1. Hi Andrew,

    These look delicious, simple and I’d love to try them. Question for you… do you suppose I could sub gluten-free flour for the wheat and agave syrup for the maple?


    • Hi Michele, I really couldn’t say about the flour… I’ve only tried them the way they’re posted. If you’re familiar with GF baking, you might be able to give it a shot. I don’t think agave would be a problem.

      • Hi again!

        Just wanted you to know that I made these over the weekend using Bob’s Red Mill Gluten Free 1-to-1 Baking Flour and the agave syrup. INCREDIBLE!! I have an autoimmune disease, so I need to be as gluten free as possible. I’ve used this flour in muffin-making and now I know it works great in cookies.

        What a wonderful recipe! So many peanut butter cookie recipes are WAY too sweet and leave that nasty little coating on your tongue. Not these cookies! Just the right amount of sweet. Very, very yummy!

        Thanks for a great recipe, Andrew.

        • Nice! I’m happy to hear that GF flour works just as well as the whole wheat flour. Thanks for reporting back and I’m so glad you liked them! 🙂

  2. AWEsome recipe, great song! Thanks for the splashes of creativity 🙂 I’m feelin’ it. Making this recipe for my boo as he is preparing for a camping trip so he has something to take along tomorrow.

  3. In the Netherlands you have very similar cookies that you can buy in the store. They look great, but taste so processed. These look amazing and you know that they will just have that superior homemade tast. Great recipe!

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