Irresistible Vegan Almond Thumbprint Cookies: Your Healthy, Gluten-Free, Refined Sugar-Free Holiday Favorite
Discover the joy of baking perfectly soft, delightfully chewy, and utterly delicious vegan almond thumbprint cookies. These cookies aren’t just a treat for your taste buds; they’re also a triumph of healthy baking! Crafted to be gluten-free, entirely free of refined sugar, and low in carbohydrates, they are the ideal guilt-free indulgence. Whether you’re planning for the festive holidays, seeking a healthy snack, or just craving something sweet and wholesome, these cookies are ready to impress in just about 30 minutes. Get ready to fall in love with a cookie that’s as nutritious as it is delicious.

This post has been updated from the original posted December 20, 2017, to provide even more details, tips, and recipe enhancements.
What Makes These Almond Thumbprint Cookies So Special?
Our almond thumbprint cookies are more than just a dessert; they’re a delightful blend of flavor, nutrition, and ease. They check every box on your cookie wish list and then some! Imagine a cookie that is:
- Perfectly Chewy and Jammy: Each bite offers a satisfying texture, with a tender almond cookie base giving way to a burst of sweet, fruity jam. The nutty taste is perfectly balanced, making them incredibly satisfying without being overly rich.
- Naturally Sweetened: Amazingly sweet without a single gram of refined sugar! We rely on natural sweeteners like pure maple syrup to achieve that irresistible sweetness, making these cookies a much healthier alternative to traditional versions.
- A Holiday Table Star: These gorgeous cookies, with their vibrant jam centers, are guaranteed to be the highlight of any holiday dessert spread. They’re a fierce, healthy competitor for the top spot, even alongside classic favorites like Vegan Ginger Cookies. Their colorful appearance makes them festive and appealing.
- Ideal for Cookie Swaps and Gifts: Be the superstar of your annual cookie swap when you bring a batch of these beauties. They look like a labor of love (even though they’re surprisingly easy to make!). Wrap them up as thoughtful, homemade gifts, and you’ll earn bonus points for sure!
- Versatile for Any Time of Year: While perfect for the holidays, I love making these cookies year-round. Raspberry chia jam is a perennial favorite, and during cranberry season, I switch to cranberry chia jam. They’re exactly what I crave with a cup of tea in the evening, yet healthy enough to grab and go for a quick breakfast.
Why These Cookies Will Become Your New Favorite

- They’re Visually Stunning! The bright, jewel-toned jam creates a beautiful contrast with the golden cookie, making them incredibly appealing and photo-worthy.
- Gluten-Free & Grain-Free (Low Carb): Made with almond flour, these cookies are naturally gluten-free and grain-free, making them suitable for various dietary needs, including low-carb lifestyles.
- The Perfect Healthy Snack: Whether it’s an after-school treat, a mid-morning pick-me-up, or a satisfying evening dessert, these cookies hit the spot without the guilt.
- Refined Sugar-Free: For those with a sweet tooth who prefer to avoid processed sugars, these cookies are a dream come true. Pure maple syrup provides natural sweetness.
- Freezer-Friendly: Planning ahead is easy! Make a double batch and freeze some for later. They thaw beautifully, so you always have a healthy treat on hand.
- Look Labor-Intensive, Are Actually Easy: Despite their elegant appearance, this recipe is incredibly straightforward to make. They offer that “labor of love” impression without the actual lengthy effort.
- Crowd-Pleasing for Cookie Swaps: They’re the ultimate cookie swap contender – unique, delicious, and healthy.
- Healthy Enough for Breakfast: Seriously! With wholesome ingredients and no refined sugar, you can enjoy one (or two!) with your morning coffee or tea without a second thought.
- Wholly Plant-Based: Made with 100% plant-based ingredients, these cookies are perfect for vegans and those looking to incorporate more plant-based foods into their diet.
- No Added Oil: We use whole food ingredients like almond butter that naturally contain healthy fats, eliminating the need for added oils.
- Deliciously Chewy with a Jammy Filling: The combination of the tender, nutty cookie and the sweet, slightly tart jam is simply irresistible.
Health Benefits of These Delicious Cookies
Beyond their amazing taste, these vegan almond thumbprint cookies pack a punch of health benefits, making them a smart choice for any occasion:
- Gluten-Free & Grain-Free: Ideal for individuals with celiac disease, gluten sensitivity, or those choosing to avoid grains for other health reasons. Almond flour provides a wonderful texture without gluten.
- No Refined Sugar: By using pure maple syrup, we avoid the blood sugar spikes and crashes associated with refined sugars. Maple syrup also contains beneficial antioxidants and minerals.
- Low Carb Friendly: Almond flour is significantly lower in carbohydrates than traditional wheat flour, making these cookies suitable for low-carb and ketogenic diets.
- Rich in Healthy Fats: Almond butter and almond flour are excellent sources of monounsaturated fats, which are heart-healthy and help keep you feeling full and satisfied.
- Good Source of Fiber: Ground flax seeds and almond flour contribute dietary fiber, promoting digestive health and helping regulate blood sugar levels.
- Plant-Based Protein: Almonds provide a good amount of plant-based protein, which is essential for muscle repair and overall body function.
- Packed with Nutrients: Ingredients like almond flour, flax seeds, and arrowroot powder offer a range of vitamins and minerals, including Vitamin E, B vitamins, and potassium.
Ingredients for Healthy Thumbprint Cookies
Traditional thumbprint cookies often come loaded with saturated fat and refined sugar. But with a few simple, smart swaps, we’ve transformed them into an easy and incredibly healthy cookie recipe! Here’s what you’ll need to create these nutritious delights:

- Almond Flour: This is the star of our gluten-free, low-carb base. Ensure you use blanched almond flour for the best texture and lightest color. It’s widely available at most grocery stores and online. Do not confuse it with almond meal, which can be coarser.
- Arrowroot Powder: A fantastic gluten-free thickener and binder. It helps give the cookies a delicate, tender crumb. Beyond its baking properties, arrowroot is also a good source of B vitamins and potassium. Cornstarch can be used as a substitute if arrowroot is unavailable, though arrowroot is generally preferred for its nutritional benefits and finer texture.
- Ground Flax Seeds: These tiny powerhouses are rich in fiber, high in Omega-3 fatty acids, and act as a binder, making them perfect for vegan and grain-free baking. They also contribute to the cookie’s slightly chewy texture and nutty flavor. Make sure they are freshly ground for optimal nutrient absorption.
- Baking Powder: Our leavening agent. It ensures the cookies rise slightly and have a pleasant, soft consistency. Always use a fresh, gluten-free baking powder.
- Smooth Almond Butter: This provides richness, healthy fats, and helps bind the cookie dough. It’s crucial to use a creamy almond butter that contains only almonds, with no added sugars or oils. Stir it well before measuring, as natural almond butter can separate.
- Pure Maple Syrup: The natural sweetener that replaces refined sugar. Opt for 100% pure maple syrup (Grade A Dark, Robust Taste is often preferred for baking). Agave nectar can be a substitute, but maple syrup offers a unique flavor profile.
- Almond Extract: Enhances the natural almond flavor of the cookies, giving them a deeper, more pronounced nutty taste. If you don’t have almond extract, you can omit it or substitute with pure vanilla extract for a different, but equally delicious, aroma.
- Sea Salt: A pinch of sea salt balances the sweetness and brings out the rich, nutty flavors of the flax and almonds. If your almond butter already contains salt, you might want to reduce or omit the added sea salt.
- No-Sugar Jam (Raspberry or Cranberry Chia Jam): The vibrant heart of our thumbprint cookies! Homemade chia jams (like raspberry or cranberry) are perfect as they contain no refined sugar and thicken beautifully. Store-bought jam with no added sugar can also be used for convenience – just be sure to read the label carefully to avoid unwanted ingredients. You can also get creative with other fruit jams like apricot or strawberry.
How to Make These Easy Thumbprint Cookies
Making these healthy almond thumbprint cookies is a straightforward process, perfect for bakers of all skill levels. Follow these simple steps to create your delicious batch:
First, preheat your oven to 350°F (175°C) and prepare a large cookie sheet by lining it with unbleached parchment paper. This prevents sticking and ensures easy cleanup.

Step 1: Combine Wet Ingredients. In a medium-sized mixing bowl, combine the creamy almond butter, pure maple syrup, and almond extract. Whisk them together until the mixture is smooth and well-incorporated. This forms the flavorful liquid base for your cookies.

Step 2: Incorporate Dry Ingredients. To the same bowl, add your dry ingredients: almond flour (or almond meal as listed in recipe card), ground flax seeds, arrowroot powder, baking powder, and sea salt. Mix thoroughly with a spatula or wooden spoon until everything is evenly combined. The dough will appear somewhat crumbly, but it should hold together easily when pressed between your fingers. If it’s too dry, add a tiny bit more maple syrup (half a teaspoon at a time).

Step 3: Roll and Shape the Cookies. Take small portions of the cookie dough and roll them into 1-inch balls (about the size of a golf ball). Place these evenly spaced on your prepared rimmed baking sheet. Next, use your thumb or the back of a small spoon (like a ½ teaspoon measuring spoon) to create a clear indent in the center of each cookie ball. This will be where your delicious jam filling goes!

Step 4: Fill with Jam. Using two teaspoons, carefully drop about 1 teaspoon of your chosen jam into each cookie indent. I highly recommend a homemade variety like Homemade Cranberry Chia Jam or raspberry chia jam for the best flavor and no refined sugar. Be gentle to avoid overflowing the indent.

Step 5: Bake to Perfection. Transfer the baking sheet to your preheated oven and bake for 13-15 minutes. Keep an eye on them; the cookies are ready when they are set and just beginning to turn a light golden brown around the edges. It’s perfectly fine if they still feel a bit soft in the center; they will firm up nicely as they cool.

Step 6: Cool Completely. Once baked, remove the cookies from the oven and let them cool on the baking sheet for about 10 minutes. This helps them set further and prevents breakage. After this initial cooling, carefully transfer them to a wire rack to cool completely. This step is crucial before storing to prevent condensation and keep them from becoming soggy.
Debra’s Pro Tips for Flawless Thumbprint Cookies

- Jam Prep Ahead: To save time, make your homemade chia jam a day or two in advance. Or, use a good quality store-bought no-sugar jam for ultimate convenience.
- Budget-Friendly Jam: Making cranberry chia jam or raspberry chia jam from scratch is not only healthier but also more economical. It’s a simple process that yields a delicious, refined sugar-free filling.
- Cool Completely for Best Results: Always allow your cookies to cool entirely on a wire rack before transferring them for storage or freezing. This prevents them from sticking together and helps maintain their texture.
- Flavor Variations: Don’t limit yourself to jam! A small dollop of melted dark chocolate (refined sugar-free, if preferred) or even a nut butter swirl can make for a delicious alternative filling.
- Double Up for Sharing (and Keeping!): If you’re baking for a cookie exchange or holiday party, consider making a double batch. That way, you’ll have plenty to share and still have some left over for yourself!
- Don’t Overbake: These cookies are best when slightly soft and chewy. Overbaking can make them dry and crumbly. They will continue to set as they cool.
- Uniform Size: For even baking, try to make your cookie balls as uniform in size as possible. A cookie scoop can be very helpful for this.
Storage Tips to Keep Your Cookies Fresh
Proper storage is key to maintaining the delicious taste and texture of your vegan almond thumbprint cookies. Here’s how to keep them fresh:
- Ensure Complete Cooling: Before storing, it’s absolutely essential that the cookies are completely cool. Storing warm cookies will create condensation, making them soggy.
- Airtight Containers are Key: Always use airtight containers to protect the cookies from air exposure, which can dry them out. Glass or plastic containers with tight-fitting lids work well.
- Prevent Sticking: To keep the jam from spreading or sticking to other cookies, place a small piece of parchment paper or wax paper between layers of cookies when stacking them in your storage container.
- Room Temperature: These cookies will stay fresh and delicious for up to 5 days when stored in an airtight container at room temperature.
- Refrigeration: For a longer shelf life, store them in an airtight container in the refrigerator for up to a week.
- Freezing for Long-Term: These cookies freeze exceptionally well! Place cooled cookies in a single layer on a baking sheet to flash freeze for about 30 minutes, then transfer them to freezer-safe zip-top bags or an airtight container. They will keep for up to 3 months. Thaw at room temperature or in the fridge before serving.
Frequently Asked Questions (FAQs)
Here are some common questions you might have about making these healthy almond thumbprint cookies:
Can I use a different type of flour?
This recipe is specifically developed for almond flour, which is grain-free and low-carb. Substituting with other flours like oat flour, coconut flour, or wheat flour will significantly change the texture and liquid requirements of the recipe. We do not recommend direct substitutions without significant adjustments to other ingredients.
What if my dough is too crumbly or too sticky?
Almond flour dough can be a bit finicky. If your dough is too crumbly and won’t hold together, try adding another ½ teaspoon of maple syrup or a tiny splash of plant milk (like almond milk) until it reaches a workable consistency. If it’s too sticky, you can add a tablespoon or two more almond flour, but be careful not to make it too dry.
Can I make these cookies without the jam?
While the jam is a signature part of thumbprint cookies, you could certainly make them without it! The cookie base is delicious on its own. Alternatively, you could fill the indent with a swirl of melted refined sugar-free chocolate after they’ve cooled, or even a dollop of a thicker nut butter for a different twist.
How can I make my own chia jam?
It’s surprisingly easy! For a quick raspberry chia jam, simply combine 1 cup of frozen raspberries, 2 teaspoons of water, 1 tablespoon of maple syrup, and ½ teaspoon of lemon juice in a small saucepan. Bring to a simmer, then cook over low heat for about 5 minutes, mashing any large berries. Remove from heat, stir in 1 tablespoon of chia seeds, and let it sit for 10-15 minutes to thicken. Store in the fridge. You can adapt this method for other fruits like cranberries or mixed berries.
More Healthy Holiday Cookie Inspiration
Looking for more delicious and healthy cookie recipes to complete your holiday spread or simply to enjoy year-round? Explore these other fantastic options:
- Gluten-free Almond Flour Biscotti
- Chewy Vegan Ginger Cookies
- Healthy Vegan Peanut Butter Cookies
- Healthier Homemade Twix Bars
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📖 Recipe

Gluten-free Almond Thumbprint Cookies
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Equipment
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Measuring Cups and Spoons
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Glass Mixing Bowls with Lids
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Half Sheet Baking Pans
Ingredients
- 1 ½ cups blanched almond flour (or fine almond meal)
- ¼ cup arrowroot powder
- ¼ cup ground flax seeds
- 1 teaspoon baking powder (gluten-free)
- ¼ teaspoon sea salt (reduce or omit if almond butter is salted)
- ⅓ cup smooth almond butter (100% almonds, no added oil/sugar)
- ⅓ cup pure maple syrup
- ½ teaspoon almond extract (or vanilla extract)
- ½ cup no sugar jam* (e.g., raspberry chia jam, cranberry chia jam)
Instructions
Make Cookies
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Preheat your oven to 350°F (175°C) and line a large, rimmed baking sheet with unbleached parchment paper.
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In a medium-sized mixing bowl, combine the smooth almond butter, pure maple syrup, and almond extract. Mix well with a spoon or whisk until the mixture is smooth and fully incorporated.
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Add the almond flour, arrowroot powder, ground flax seeds, baking powder, and sea salt to the bowl. Mix thoroughly until all dry ingredients are fully combined with the wet mixture. The dough will have a slightly crumbly texture, but it should easily press together between your fingers. If it feels too dry, add an additional ½ teaspoon of maple syrup at a time until pliable.
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Roll the cookie dough into uniform balls, roughly the size of a golf ball (about 1 inch in diameter). This recipe should yield approximately 18-24 cookies, depending on their size. Place them evenly spaced on your prepared baking sheet.
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Using your thumb or the back of a small teaspoon, create a distinct indent in the center of each cookie ball. Carefully fill each indent with about 1 teaspoon of your chosen no-sugar jam.
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Bake for 13-15 minutes, or until the cookies are set around the edges and just beginning to turn a light golden brown. They may still feel soft in the center, which is perfect as they will firm up further upon cooling.
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Let the cookies cool on the baking sheet for about 10 minutes before carefully transferring them to a wire rack. Allow them to cool completely on the rack before storing to prevent stickiness and preserve their texture.
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Store cooled cookies in an airtight container in the refrigerator for up to 1 week, or freeze them for up to 3 months. When freezing, place parchment paper between layers to prevent sticking.
Notes
Homemade Raspberry Chia Jam Recipe:
- 1 cup frozen raspberries
- 2 teaspoons water
- 1 tablespoon pure maple syrup
- ½ teaspoon lemon juice
- 1 Tablespoon chia seeds
To make your own delicious and healthy jam, place the frozen raspberries, water, maple syrup, and lemon juice into a small saucepan. Bring the mixture to a gentle simmer over medium heat, then reduce heat to low and cook for about 5 minutes, stirring occasionally. Use the back of a wooden spoon to mash any berries that haven’t naturally broken down. Turn off the heat, stir in the chia seeds, and let the mixture sit for at least 10 minutes to allow it to thicken to a jam-like consistency. Stir again before using. This homemade chia jam can be stored in an airtight container in the fridge for up to a month.
For variations, you could also use a homemade cranberry chia jam or a good quality store-bought jam. If opting for store-bought, always be sure to carefully read the label to ensure there are no added refined sugars or unwanted artificial ingredients.
Nutrition
Note
The nutrition calculations were done using online tools. To obtain the most accurate representation of the nutritional information in any given recipe, you should calculate the nutritional information with the actual ingredients you used. You are ultimately responsible for ensuring that any nutritional information is accurate, complete and useful.