Chewy and fudgy, these vegan cream cheese stuffed pumpkin cookies showcase all the delicious warm flavors of fall. It’s also gluten-free, vegan, and made using good-for-you almond and coconut flours.

I’m obsessed with stuffed cookies. I especially love the surprise people get when they bite into a cookie and find out – hey, there’s more!
People seemed to like my cream cheese stuffed strawberry cookie recipe a lot, so I just had to find a way to incorporate some of my favorite fall flavors into a stuffed cookie recipe 🙂
Made with almond flour and coconut flour, these cookies are chewy, fudgy–almost hearty! It’s perfect for whenever I’m craving a mid day snack.



Ingredients used to make these
**I’ve linked some of these ingredients to amazon.com to give you an idea of what they are, but you should be able to find them in your local grocery store (usually, the natural & organic food section). They are also affiliate links, which means that I earn a commission as an Amazon Associate if you decide to purchase the items. The price will be the same to you, link or no link 🙂
- Almond flour – I used blanched almond flour
- Coconut flour – coconut flour does not substitute well, and I can’t recommend swapping coconut flour with other ingredients unless you absolutely had to (2 Tbsp coconut flour = ½ cup almond flour). Unfortunately, you probably won’t get the same texture or mouthfeel as the original recipe.
- Pumpkin puree – I used canned pumpkin puree
- Eggs – I used regular large eggs
- Salt – Pink Himalayan salt is what I have at home, so it’s what I use, but you can use any kind for this recipe. Since I use only a small amount, the conversion (between kosher and fine salt, for example) isn’t necessary.
- Coconut Sugar – You can use any granulated sugar for this recipe. Coconut, date and maple sugars are less processed sugars I would recommend. Honey and maple syrup should also work, but I have not yet tried. For keto options, you could also use stevia (but be sure to convert according to package instructions). I also put a range on the amount you could use (3 to 5 Tablespoons) because I personally prefer desserts that aren’t overwhelmingly sweet. I would say 3 Tbsp is subtly sweet, 4 Tbsp is sweet enough, and 5 Tbsp is sweet.
- Vegan Cream cheese – I used vegan cream cheese made from almond milk, but you could also use regular cream cheese. For a paleo friendly option, you can also make your own “cream cheese” with soaked cashews.

Recipe Variations and Optional Add Ins:
- You can add replace the coconut sugar with molasses and add ½ tsp of gingerbread spice instead of the pumpkin pie spice to make these cookies gingerbread flavored!
- There are so many different ways you can flavor the cream cheese filling. Here are some ideas of flavorings you could add to the cream cheese in addition to the stevia called for in the recipe:
- 1 tsp of cinnamon, or
- 2 Tbsp almond butter, or
- 1 tsp fresh or dried orange zest,
- or my personal favorite—1 tsp of powdered instant coffee!
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- Plain, warm or cold
- Drizzled with almond or pecan butter
- Frosted with my healthy chocolate frosting or almond butter frosting

How to Store
Because of the cream cheese, I wouldn’t recommend storing this cookie in room temperature for more than a day. Store it in the refrigerator up to 5 days, or freeze them up to 4 months. When you’re ready to eat, you can defrost overnight in the fridge or at room temperature.
Final Tips
- Baking time will vary based on how thin or wide you make your cookies. Bake the cookies until the tops are dry and the bottom of the cookies are golden-brown
- How to stuff: Scoop about 2 tablespoons of dough onto parchment lined cookie pan, flatten like a disk, then top with 1-2 Tbsp of cream cheese filling then use another 2-3 tablespoon of cookie dough (also flattened like a disk) to cover filling entirely.

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Healthy Cream Cheese Stuffed Pumpkin Cookies (Gluten-free, Vegan)
Ingredients
DOUGH
- ¼ cup ground flaxseed meal
- 1/2 cup hot water
- 2 cups almond flour
- ¼ cup coconut flour
- 1/4 tsp salt
- 1/3 cup granulated sugar or sweetener of choice*
- 1/2 cup pumpkin puree
- 1/2 cup light olive oil
FILLING
- 1 6 oz container of vegan cream cheese
- 1/16 tsp of pure stevia** powder or 3 packets of stevia
Instructions
- First, make the flax egg by mixing the ground flax and water then let sit 5 minutes.
- In another bowl, mix all the dry ingredients together, then add the rest of the wet ingredients (including the prepared flax egg) until dough is smooth.
- Chill in the fridge for 10-30 minutes,
- Meanwhile, prepare the cream cheese filling by mixing the cream cheese with stevia**
- Scoop about 2 tablespoons of dough onto parchment lined cookie pan, flatten like a disk, then top with 1-2 Tbsp of cream cheese filling then use another 2-3 tablespoon of cookie dough (also flattened like a disk) to cover filling entirely.
- Bake in oven 350F for about 13-15 or until slightly golden with browned cookie base.
- Let cool before eating and store in fridge to eat later.
Notes
Nutrition

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