This Paleo Chocolate Pecan Pie has a flaky grain-free pie crust and a layer of chocolate ganache! This gluten-free and refined sugar-free pie is gooey, crunchy, and the perfect addition to your holiday dessert line-up.

So, I have a pie recipe that you’ve got to add to your Thanksgiving line-up. It’s not just me insisting it – I just got a FaceTime call from my Aunt Tara, dying to show me her lunch: a big slice of this chocolate pecan pie. She works with my dad, and I sent this pie along with some of my homemade twix bars to work with him.
She was obsessing over it, declaring it the best thing I’ve ever made and insisting it be made again for Thanksgiving. She’s had a LOT of the things I’ve made over the years, so that’s saying a lot. Needless to say, it’ll definitely be making an appearance on our Thanksgiving dessert table.

Pecan pie has always been one of my favorite Fall pies, right up there with apple. In fact, I already have two pecan pie recipes on Bakerita – this less healthy but delicious brown butter pecan pie, and this paleo pecan pie. I couldn’t help but create another version for this year’s Thanksgiving, and chocolate (as usual) was calling to me.
To give this pecan pie a chocolatey twist, a layer of rich chocolate ganache is spread on the bottom crust before the pecan filling is added. After it bakes up, you get this nice gooey layer of chocolate in the midst of the pecan-packed filling. So swoon-worthy.

I love the crust recipe that I used here too – it’s super flaky, and as far as grain-free pie crusts go, pretty easy to work with. And bonus! If its breaks, you can press it back together super easily. There’s no gluten to overwork, so small chance of a super tough crust.
The filling is obviously corn syrup free, instead using maple syrup and coconut sugar to sweeten. In most pecan pies, I hate the weird gelatinous layer of sugary goo, but in this one, it has flavor and while it’s sweet, it isn’t cloyingly so.

This chocolate pecan pie has got to be well chilled before you cut into it, or you might have a gooey mess on your hands. I was impatient in cutting the pie in the pictures, which is why my slices aren’t perfect. If you have more patience than me, you’ll have beautiful slices! This can definitely be made the day before serving, and I’d recommend doing so.
I sprinkled on a bit of Maldon flaky sea salt after I took pictures (oops) and it gave a little salty bite that I’m a big fan of (my aunt also loved the salt, in case you were wondering 😉). Besides that, a bit of unsweetened whipped cream or coconut cream is really all you need to pair with this.

Pair it with this paleo pumpkin pie for some healthier but oh so delicious Thanksgiving desserts :) hope you love this one! Enjoy!
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Paleo Chocolate Pecan Pie
Ingredients
- 1½ cups (144g) almond flour
- ½ cup 57g tapioca flour
- 1 tablespoon coconut sugar
- ¼ teaspoon kosher salt
- 6 tablespoons cold grass-fed butter, cubed
- 1 egg, cold
For the chocolate layer
- 4 oz. dark chocolate, chopped
- ¼ cup canned coconut milk
For the pecan filling
- ¾ cup coconut sugar
- ¼ cup maple syrup
- ⅓ cup coconut oil, melted
- 2 eggs, room temperature
- 1 tablespoon almond flour
- 1 tablespoon almond milk, or any non-dairy milk
- 1 teaspoon vanilla extract
- ¼ teaspoon kosher salt
- 2 cups pecans, chopped
Instructions
For the crust
- Combine the almond flour, tapioca flour, coconut sugar, salt and butter in a food processor, or use a pastry blender in a bowl. Pulse or blend until the texture of coarse meal.
- Add 1 egg and pulse/mix again until dough comes together. If you’re mixing in a bowl, you may want to use your hands to bring the dough together at the end.
- Press the dough into a disk and wrap in plastic wrap. Turn out the dough onto a piece of plastic wrap and refrigerate for at least 1 hour or up to a few days.
- When ready to bake, roll out your dough in between two sheets of parchment into a 12-inch circle. Lay dough into a 9-inch pie dish (NOT deep dish) and place in the freezer while you prepare the filling.
For the filling
- Preheat the oven to 325°F.
- Place the finely chopped chocolate in a bowl. Microwave the coconut milk until it’s bubbling, about 30 seconds. Pour over the chopped chocolate, making sure all of it is submerged, and let stand for 1 minute. Whisk until smooth.
- Spread the chocolate ganache evenly on the bottom of the frozen pie crust and return to the freezer.
- In large bowl, beat the eggs until slightly foamy. Stir in the coconut sugar, maple syrup, and coconut oil. Whisk together until fully combined. Stir in the almond flour, almond milk, vanilla and salt. Add the pecans and stir until they are fully coated.
- Remove the pie crust from the freezer and fill with the pecan filling.
- Bake in the preheated oven at 325°F and bake for 45-50 minutes, or until the top no longer jiggles in the center. Let cool on a wire rack for one hour, and then move to the refrigerator to cool completely before slicing and serving.

Hi! I am a baking beginner and making your pie today! I refrigerated the crust dough overnight. I took it out to start working with it this morning and I think I let it warm up too much. When I rolled it out, the crust fell apart easily and I couldn’t peel it off the parchment paper. So I shaped it back into a disk and put it back in the fridge again. Hopefully it will work! Do you have any other thoughts or suggestions? Thanks!
Hi Liz, it definitely helps to have a cooler crust when you’re rolling out or it will fall apart easily, as you experienced. Since there’s no gluten in it, it should be totally fine to chill and try again :) just make sure to keep it relatively cool while rolling out, and I like to roll out on parchment and then place the pie tin on top of the crust, and flip the whole thing over to make things easiest. It will break a little bit since there isn’t any gluten to hold things together, but you can press it back together with your fingers without issues. Hope this helps – Enjoy!!
Thank you, Rachel! It still broke apart a bit then 2nd time. But I did the trick you mentioned, and it really helped. I just pressed the crust back into the pie dish. We’ll be digging in soon! The recipe was very easy to follow. Thank you!
Hi Rachel! I’m excited to try out some of your recipes! Do you think flax egg or an egg replacer would work in this recipe? My son is allergic to eggs, as well as wheat & dairy.
Hi Rachel, in this recipe I would use the following instead of eggs and the 1 tbsp almond milk: ⅓ cup non-dairy milk, 2 tablespoons flax meal, 2 teaspoons arrowroot starch or tapioca flour. Just whisk in with the rest of the ingredients. Enjoy! :)
Can I use the this recipe or the Paleo pecan pie recipe to fill muffin cups instead of a pie pan to make mini pies?