Made with oat flour, almonds, pecans, and peanut butter, these healthy thumbprint cookies are the perfect low-sugar, high-fiber treat to enjoy any time of year! The strawberry chia jam adds a pop of brightness and gorgeous color that gives these cookies a nostalgic peanut butter & jelly flavor. Perfect for satisfying your sweet tooth or whenever you need a snack on the go! {Vegan, dairy-free & gluten-free}
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Healthy Thumbprint Cookie Recipe
When you find yourself in the middle of baking season and in desperate need of a sweet treat, these cookies will do the trick!
The ingredients are more like what you’d find in granola bars – oat flour, ground nuts, and peanut butter – which is part of what gives the cookies a soft and chewy texture, but with lots of nuttiness.
For an extra pop of sweetness, I like to fill them with homemade strawberry chia jam, but you can easily substitute your favorite jam whether it’s homemade or store-bought.
Between the nutty cookie dough and sweet jammy goodness, you won’t believe they’re a healthier option!
For more healthier cookie recipes, be sure to try my Healthy Shortbread Cookies and 3-Ingredient Peanut Butter Blossoms too!
Before You Get Started
These tips will help ensure your cookies turn out extra delicious!
- Be patient when blending: When blending the almonds, pecans and shredded coconut, you may need to blend it for several minutes before it begins to form a paste. The mixture might start to stick to the sides of the food processor. In that case, stop the food processor, push the mixture off the sides with a spatula and continue to blend until a paste-like consistency has formed.
- Allow the cookies to cool: The cookies will feel really soft to the touch when you remove them from the oven. It’s very important that you allow them to cool completely before removing them from the pan so that they have a chance to firm up.
- Purchase pre-made oat flour or make your own: You can find oat flour in most grocery stores, or make your own by blending oats in a blender until it forms a flour-like consistency.
- Prepare jam in advance: I love using my 4-ingredient strawberry chia seed jam for these cookies since it’s lower in sugar and less processed than most jams. If you choose to go the chia seed jam route, I recommend making it in advance so that you just have to plop it into the center of each cookie when ready to bake. Even if you don’t make it in advance, it’s super easy to prepare. Alternatively, you can use your favorite homemade or store-bought jam.
Why We Love These Chia Jam Thumbprint Cookies
- Quick & easy: These soft, chewy jam cookies come together fast and bake in no time. They’re also a fun, hands-on recipe for kids to help with.
- Nutritious snack: Made with nuts, coconut, and oats, these cookies offer protein, fiber, and healthy fats to help keep you satisfied.
- So delicious: Proof that healthy can still be crave-worthy! The combination of nuts, coconut, and maple syrup makes these cookies so rich and cozy!
Ingredient Notes
- Nuts: I use a mix of raw almonds and pecans in the cookie dough for a diverse nutty flavor. You can use one or both, or try using different nuts too!
- Shredded coconut: This helps to naturally sweeten the cookies and adds a lovely flavor that complements the rest of ingredients so well. Use unsweetened fine or medium shredded coconut or coconut flakes.
- Oat flour: Use oat flour to add some fiber to these cookies and help act as a binding agent.
- Salt: A pinch of salt brings out the natural sweetness.
- Peanut butter: For a healthier option, use a natural peanut butter; not one with added salt and sugar. You can also sub in almond butter or cashew butter if desired.
- Pure maple syrup: To sweeten the cookies and help bind the ingredients together. If you don’t require a vegan option, you can also use honey.
- Vanilla extract: Use pure rather than artificial.
- Jam: I love using a chia seed jam for added nutrients, but you can use any fruit jam you have on hand.
How to Make Peanut Butter Thumbprint Cookies with Jam (Plus Helpful Tips!)
- Get Ready to Bake: Preheat your oven to 350°F (175°C) and line a baking sheet with parchment paper. This makes cleanup a breeze and helps ensure your cookies don’t stick.
- Blend the Nuts: Add the raw pecans and almonds to a food processor or high-speed blender and pulse until they’re finely ground. This builds a nutty base for your dough. Tip: If the nuts cling to the sides, pause and scrape them down with a spatula so everything gets evenly processed.
- Add Coconut: Toss in the unsweetened shredded coconut and continue blending until you get a paste-like texture. This natural sweetness and texture boost keeps your cookies rich without added sugar.
- Mix the Dough: Transfer the nut-coconut mixture to a bowl. Add oat flour and a pinch of salt and stir to combine. Then mix in peanut butter, maple syrup, and vanilla until everything forms a slightly sticky and cohesive dough.
- Shape Your Cookies: Scoop out about 1½-inch balls of dough — I like to use a small cookie scoop — and roll them between your palms. Arrange the balls about 1 inch apart on your prepared baking sheet.
- Make the Thumbprints:Press your thumb (or the back of a small spoon) gently into the center of each ball to create an indentation. Tip: If the edges crack a little, just press them back together with your fingers!
- Add the Jam: Spoon about 1 teaspoon of jam into each indentation. A classic strawberry chia jam works wonderfully, but feel free to use your favorite flavor. Pro tip: Don’t overfill — too much jam can spill over as the cookies bake.
- Bake to Perfection: Slide the tray into your preheated oven and bake for 10–12 minutes. For softer, gooier centres, stick with the shorter time; bake a bit longer if you want firmer cookies.
- Cool Before Enjoying: Once baked, let the cookies cool on the sheet for at least 20 minutes before transferring them to a rack. This cooling time helps them firm up so they’re easier to lift without breaking apart.
Scroll to the recipe card below for the full-printable recipe!
Storage Guidelines
Since these cookies are filled with a raw jam, I’d recommend storing them in an airtight container in the fridge for up to 1 week.
You can also store them in a freezer safe bag or container for up to three months. If stacking them, place a piece of parchment paper in between the cookies to prevent them from sticking together. Thaw them at room temperature when you’re ready to serve and enjoy.
Topping Ideas
If you want to make your cookies even fancier or switch up the flavors, you can always add some additional toppings.
You can drizzle the baked cookies with melted dark chocolate, fill them with lemon curd or apple butter or add a light sprinkle of icing sugar.
You can even make them into heart thumbprint cookies. Feel free to get creative!
Serving Suggestions
For a holiday treat, I like to pair these cookies with my non alcoholic christmas punch or homemade hot chocolate with chocolate chips.
During the warmer months of the year, you may want to try adding a strawberry banana smoothie to play up the berry flavors. So refreshing!
Recipe variations
- Nut butter: Instead of peanut butter, you can also use almond butter or cashew butter.
- Sweetener: If you don’t need the cookies to be vegan, you can use honey instead of maple syrup.
- For extra nutty flavor: Add a bit of almond extract.
More Healthy Cookies
If you want something else to try, these 3-Ingredient Almond Flour Cookies make a great holiday dessert. I’m also a big fan of these Raw Cookies made with peanut butter, chocolate chips, and dates.
During spring and summer, I often switch to these Lemon Almond Flour Cookies, which are soft, chewy, and so lemony!
Did you make this recipe? Scroll down to leave a star rating and review!
Peanut Butter Thumbprint Cookies with Jam
Ingredients
- 1/2 cup raw almonds
- 1/2 cup pecans
- 1/2 cup unsweetened shredded coconut
- 1/3 cup oat flour plus 2 tablespoons
- 1/4 teaspoon salt
- 1/4 cup natural peanut butter
- 1/4 cup maple syrup
- 1 teaspoon pure vanilla extract
- 1/4 cup strawberry chia jam (or sub in your favorite homemade or store-bought jam)
Instructions
- Preheat the oven to 350 degrees F. Line a baking sheet with parchment paper.
- Add the pecans and almonds to a food processor or high power blender and blend until the nuts are finely broken down.
- Next, add in the shredded coconut. Blend together until a paste-like consistency is achieved, scraping off the sides with a spatula every once in a while to ensure that all of the mixture is blended.
- Transfer the "paste" to a medium mixing bowl and add the oat flour and salt. Mix until combined. Add in the peanut butter, maple syrup and vanilla and mix until well combined. The mixture should form a slightly sticky dough.
- Roll the mixture into 12 balls that are about 1 ½ inches in diameter. Place the balls on the lined baking sheet about 1 inch apart.
- Place your thumb in the centre of each cookie, pressing down gently until a slight indent is formed. If the outside of the cookies start to crack a bit, gently mold the mixture back together again.
- Fill the centre of each cookie with about 1 teaspoon of jam, spreading it out slightly so that it covers the indent.
- Place the cookies in the oven and bake for 10-12 minutes. I prefer to bake my cookies for 10 minutes for a softer cookie and more gooey centre, but you can bake for longer if you prefer a firmer cookie.
- Allow to cool for at least 20 minutes or until completely cooled before removing from baking sheet. This step is VERY important as it allows the cookies to firm up since they’ll be very soft when they come out of the oven.
Notes
- Be patient when blending: When blending the almonds, pecans and shredded coconut, you may need to blend it for several minutes before it begins to form a paste. The mixture might start to stick to the sides of the food processor. In that case, stop the food processor, push the mixture off the sides with a spatula and continue to blend until a paste-like consistency is achieved.
- Allow the cookies to cool: The cookies will feel really soft to the touch when you remove them from the oven. It’s very important that you allow them to cool completely before removing them from the pan so that they have a chance to firm up.
- Purchase pre-made oat flour or make your own: You can find oat flour in most grocery stores, or make your own by blending oats in a blender until it forms a flour-like consistency.
- Prepare jam in advance: I love using my 4-ingredient strawberry chia seed jam for these cookies since it’s lower in sugar and less processed than most jams. If you choose to go the chia seed jam route, I recommend making it in advance so that you just have to plop it into the centre of each cookie when ready to bake. Alternatively, you can use your favorite homemade or store-bought jam.
Nutrition
This recipe was originally posted in November 2021 and was updated in December 2023 to include more helpful tips and photos. The text, formatting and some photos were updated again in December 2025.
Hello! Was going to make this—but not a fan of coconut. Is it ok to just omit? Or do I need to sub something else in place of it? Any suggestions of what is good to sub if so? Thank you!
Love this recipe! Such a great healthy alternative to the normal thumbprint cookies which are made with sugar, butter and white flour! In fact it tastes better! Thanks Elysia for a great healthy treat!♥️♥️♥️
So happy you enjoyed the recipe! These cookies are always a hit in our house too! Thanks so much for returning to leave a review :)