These Keto Peanut Butter and Jelly cookies are some of the most fun (& tasty!) low carb thumbprint cookies out there! Easy to make, too!
Last year, I decided to use that classic peanut butter cookie base to create a new recipe for buttery peanut butter cookies.
Based around a favourite childhood sandwich, these chewy peanut butter cookies are basically a pb&j sandwich, in cookie form!
The thumbprint style of cookie lends itself really well to the classic flavor pairing, with chewy peanut butter cookies making a great base for the little hit of jam on top of each.
It’s a great recipe for the holiday season, because it’s something that everyone loves - whether they’re gluten free and/or low carb themselves, or not. It’s always nice to be able to serve a single batch of cookies to a mixed crowd - they’re dietarily inclusive!
About the Carb Count
About 4.5 grams of carbs per cookie are coming from the allulose (deductible).
Add that to the 1 grams of fiber, and you're left with about 2.5 net grams of carbs per cookie!
Anyway, let’s look at the ingredients you’ll need for this low carb, gluten free peanut butter and jelly cookie recipe!

Ingredients
This keto PB&J cookie recipe uses fairly simple ingredients, for anyone that’s been doing any keto baking. You shouldn’t have any trouble finding everything you need in any larger grocery store.
As always, I have a few ingredient notes for you:
Smooth Peanut Butter
All of the peanut butter flavor in these chewy cookies comes from the creamy peanut butter used.
Look for a natural peanut butter without added sugar, when possible.
Also, if you REALLY want to use crunchy peanut butter, you’ll need to use a bit extra, to make up for the volume lost to the peanut pieces.
I’d add probably 2 tablespoon - ¼ cup worth, and see how that goes.
Sugar Free Raspberry Jam
As jelly thumbprint cookies, there are all kinds of different jams and jellies you can use. It’s just a matter of which favorite jelly fits your macros!
I use sugar free raspberry preserves, as that’s my favourite of the low sugar jam options locally. I can usually find some store of strawberry jelly / strawberry preserves / strawberry jam, which also works well.
grape jelly would also be fantastic, I just haven’t happened across a sugar free version, locally!
Maybe sugar free blueberry jam would be a decent alternative? I’ve never used blueberry jam in peanut butter & jelly sandwiches, though!
The “Flour” Mixture
I use a mix of 3 flour alternatives - Super Fine Almond Flour, Vanilla Flavored Whey Protein Powder, and Coconut Flour - along with a little Xanthan Gum.
This is pretty much by go-to mix to replace all purpose flour in my keto cookie recipes. It’s low carb, tastes great, gives you a great texture, and you even get a bit of protein out of it!
As far as the protein powder goes, I use Revolution Nutrition's High Whey in Vanilla Cake, but any brand should work.
Just be sure to use one that you love the taste of, and that suits your macros.
Sweeteners
I use two different sweeteners in this keto cookie recipe, for the best peanut butter cookies possible. Much more like my traditional peanut butter cookies, than just using a white sugar substitute.
For me, this means using both Brown Allulose - as a brown sugar replacement - and Granulated Allulose, as a white sugar replacement.
When using allulose, I use ⅓ cup each.
If you’d prefer to use Erythritol / Monkfruit Blend Sweeteners - like Swerve Granular Sweetener and Swerve Brown Sugar Substitute - use ¼ cup instead.
Personally, I’m not a fan of the taste / mouth cooling sensation that comes with erythritol. Also, there’s been some concerning data coming out about it in the past few years.
Everything Else
Rounding out this recipe, you will need:
Unsweetened Almond Milk (or other milk of choice)
Large Eggs
Pure Vanilla extract
Baking Powder
Xanthan Gum
Baking Soda
Salt
... I just don’t have anything else to add, as far as these last few ingredients go!

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How to Make Keto Peanut Butter & Jelly Cookies
The full recipe is in the printable recipe card at the end of this post, here is a visual walk through.
Keto Peanut Butter Cookie Dough:
In stand mixer fit with a paddle attachment - or in a large mixing bowl if using an electric hand mixer - cream butter, peanut butter, and sugar substitutes on medium-high speed until fluffy.
Add eggs, milk, and vanilla, beat until everything is fully incorporated and smooth.

In a separate bowl, mix together remaining ingredients.

Slowly add this dry ingredients mix to the mixer bowl of wet ingredients, and carefully mix until well incorporated and smooth.

Wrap with plastic wrap, let dough chill for 1 hour.

Making the Keto Peanut Butter Thumbprint Cookies
Preheat the oven to 350 F, line baking sheets with parchment paper.
Roll 1" balls of cookie dough, or use a cookie scoop. You want to get about 30 cookies from the batch.
Arrange dough balls on a prepared baking sheet, leaving at least 2" between cookies - they flatten out a fair amount.
If you don’t leave enough space, you might end up with conjoined cookies! Note: The degree of spread can vary based on the sweetener used.

Use your thumb to form a round, shallow indentation center of each cookie.

Bake for 11-13 minutes. Cookies will be golden brown and look puffy, but they flatten out as they cool. For best results, do not over bake!

Cool completely before storing in an airtight container.
Once cooled to room temperature, cookies can be stored in an airtight container for a few days on the counter, longer if in the fridge.

More Keto Cookie Recipes
Looking to indulge your sweet tooth in a way that won’t spike your blood sugar? Here are some delicious recipes for low carb cookies to try!
Apple Pie Cookies
Biscotti
Candy Cane Cookies
Chocolate Chip Cookies
Chocolate Peanut Butter Cookies
Chocolate Protein Cookies
Cowboy Cookies
Gingerbread Cookies
Ladyfingers
Lemon Cookies
Peanut Butter Chocolate Chip Cookies
Peanut Butter Pecan Chocolate Chip Cookies
Pecan Pie Cookies
Pumpkin Spice Cookies
Red Velvet Cookies
Rolled Sugar Cookies
Snickerdoodles
Soft Peanut Butter Cookies
Sugar Free Royal Icing
Triple Chocolate Cookies
Valentine’s Chocolate Thumbprint Cookies
White Chocolate Peppermint Cookies
Witch Finger Cookies
... but wait, there's more! We have a desserts section for keto recipes - Keto Dessert Recipes! Check it out!

Keto Peanut Butter & Jelly Cookies [Low Carb & Gluten Free]
Equipment
- 2 large baking sheets
- Parchment paper
Ingredients
- ¾ cup Smooth peanut butter
- ⅓ cup Brown Allulose ¼ cup for erythritol blend
- ⅓ cup Granulated Allulose ¼ cup for erythritol blend
- 2 Large eggs
- 1 tablespoon Unsweetened Almond Milk
- 2 teaspoon Vanilla extract
- ½ cup Superfine Almond Flour
- ½ cup Vanilla Whey Protein Powder
- ¼ cup Coconut flour
- ½ teaspoon Baking powder
- ½ teaspoon Salt
- ½ teaspoon Xanthan gum
- ¼ teaspoon Baking soda
- ¼ cup Sugar free Raspberry Jam
Instructions
Keto Peanut Butter Cookie Dough:
- In stand mixer - or in a large bowl if using an electric mixer - cream butter, peanut butter, and sugar substitutes until fluffy.
- Add eggs, milk, and vanilla, beat until everything is fully incorporated and smooth.
- In a separate medium bowl, mix together remaining ingredients.
- Slowly add this dry ingredients mix to the mixer bowl, and carefully mix until well incorporated and smooth.
- Cover dough with plastic wrap, chill for 1 hour.
Making the Keto Peanut Butter Thumbprint Cookies
- Preheat the oven to 350 F, line baking sheets with parchment paper.
- Roll 1" balls of cookie dough, or use an ice cream scoop. You want to get about 30 cookies from the batch.
- Arrange dough balls on a cookie sheet, leaving at least 2" between cookies - they flatten out a fair amount.
- Gently press the tops of each slightly - flatten JUST enough to prevent the dough from rolling.
- Use your thumb to form a round, shallow indentation in the center of the dough.
- Fill each indentation with about 1 teaspoon of sugar free raspberry jam.
- Bake for 11-13 minutes. Cookies will look puffy, but flatten out as they cool. Do not over bake!
- Allow cookies to cool for 2 minutes before removing from baking sheets. You can transfer them to a cooling rack, if you like.Cool completely before storing in an airtight container.
- Once cooled to room temperature, cookies can be stored in an airtight container for a few days on the counter, longer if in the fridge.
Notes
Nutrition

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A fun cookie recipe, that satisfies multiple cravings at once! Hope you love the recipe as much as we do!