Healthy Pecan Pie Bars are one of the best pecan pie recipes! Gluten free, paleo and refined sugar free – an easy holiday dessert you’ll love!

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When we got a request for holiday desserts, we took it seriously. From Apple Crumble Bars to Pumpkin Pie Bars, we’ve covered almost all the bases.. but we couldn’t forget pecan pie!!
If you’re searching for other Holiday Recipes – check out these 50 Healthy Thanksgiving Recipes or Healthy Christmas Recipes!
Pecan pie is something I sadly didn’t grow up eating (my brother is allergic to nuts) but when I first tried it a few years ago I fell in love.
A buttery crust filled with sweet pecans.. uh yeah, count me in. This year we wanted to bring you a pecan pie that has ALL that flavor, with cleaned up ingredients
These taste just like the classic pecan pie while being totally paleo, dairy free, gluten free, grain free, and lower in sugar.
Note: This recipe is a bit more involved than compared to our other recipes – but it’s well worth the extra time! I think you’re going to love them!
Pecan Pie Bar Video:

What makes these pecan pie bars healthier?
Calorie for calorie, these bars are not very different from a classic pecan pie bar. Pecans are a high calorie food, and they’re the main ingredient.
These bars are not something we’d recommend eating every day, but they do have a few things that make them different from classic pecan pie
- Sugar: Most pecan pie bars have 40-50 grams of sugar, while these bars have 22g. 22g of sugar is still A LOT of sugar, but almost half the amount of classic pie!
- Ingredients: Classic pecan pie is made with a ton of corn syrup. These bars have no corn syrup and considerably less sugar.
- Lower Carb: These bars are not low carb, but classic pecan pie has about 65g of carbs per slice, while these only have 37g of carbs per bar.
This has nothing to do with them being healthier, but these bars are also A LOT easier to make than regular pie. Who has time for rolling out pie crust? Not me.

Ingredients for Healthy Pecan Pie Bars
To make these healthy pecan pie bars you’ll need:

These bars are gluten free, dairy free, nut free, soy free, refined sugar free, and grain free. You can’t substitute the flours in this recipe. See the green box below for notes on substitutions.
We recommend making these in a metal 8×8 baking pan.
How to make Paleo Pecan Bars
To make these Paleo Pecan Bars first we’ll make the crust.
- Mix together the ingredients for the crust.
- Press your dough into your pan & bake.
- While the crust bakes – make the filling.
- Pour the pecan mixture into the crust and bake at 350 for 15-17 minutes.
- Allow the bars to cool on the counter for 1 hour.
- Transfer to the fridge for at least 2 hours before you cut it.

Serving Gluten Free Pecan Bars:
These Gluten Free Pecan Bars are perfect on their own but we really love the Maldon sea salt at the end. The salty/sweet combo is so delish!
Serving: We recommend serving these with whipped cream and vanilla ice cream. Feel free to sub in dairy free if necessary. These bars are also great plain!
Serving Size: I divided this into 9 pecan pie bars, but you can also cut them into 16 if you’d prefer smaller pecan pie bars.

Substitutions Healthy Pecan Bars
We love to provide substitutions for our recipes, but this recipe is pretty specific and there aren’t many substitutions I can provide.
If you make these bars as is you’ll wind up with perfect gluten free, paleo, lighter pecan pie bars – but if you make swaps you might wind up with a mess!
Baking pan: This recipe was tested in both glass and metal baking dishes. Metal conducts heat far better than glass so it was finished quicker! Make sure you follow instructions to avoid the bars from sticking!
Flour: I don’t recommend other flours for the crust, especially almond flour. The curst is a tried and true formula of coconut and tapioca. The tapioca provides a binder along with the egg. this crust is very cookie like!
Eggs: You can’t substitute eggs in the crust for this recipe.
Ghee: Ghee was used for flavor. We don’t recommend coconut oil for a swap because you won’t get the same flavor and it is very greasy. Grass fed butter or regular butter would be good swaps for the ghee. I have not tried dairy free butter.
Maple syrup: Honey can be used in place of maple syrup in the filling but it will have a different flavor.
Coconut Sugar: Brown sugar can be used in place of coconut sugar if you’re not paleo.
Doubling the recipe: I haven’t tried doubling the recipe, but I think it would work in a 9×13 pan.
Almond Milk: You can substitute regular milk in place of almond milk if you’re not dairy free.

I mean… don’t you just want to take a bite?!
How to store paleo pecan pie bars:
Gluten Free Pecan Pie Bars should be stored in the refrigerator. They will last in the refrigerator for up to a week.
Heating: If you like warm pecan pie just heat in the microwave for 10-20 seconds.
Freezing: I haven’t tried freezing these pecan bars but I don’t think they would freeze well in an airtight container.

We hope you love these pecan pie bars just as much as we did!
We love to enjoy with a mug of warm Healthy Hot Chocolate!
Pecan Pie Bar FAQ
Pecan pie is loaded with sugar and fat which is what makes it ‘bad for you’. I believe in everything in moderation, but these pecan pie bars are lower in fat, sugar and carbs.
Yes! You can make pecan pie the night before! It’s actually better to do that so your pecan pie can set.

Other healthy dessert recipes:
If you’re looking for other healthier desserts – check out this blog post with 30 Healthy Holiday Desserts, or any of these!

Healthy Pecan Pie Bars
Ingredients
Crust:
- 1/4 cup maple syrup
- 1/3 cup melted ghee *cooled* or butter
- 1 large egg
- 2 teaspoon vanilla extract
- 2/3 cup coconut flour
- 1/4 cup tapioca flour
- 1/4 teaspoon salt
Filling:
- 1/2 cup melted ghee or butter
- 1/3 cup maple syrup
- 2/3 cup coconut sugar or brown sugar
- 3 teaspoons vanilla extract
- 2 tablespoons unsweetened almond milk
- 2 1/2 cups chopped pecans
- 1/8 teaspoon salt
- Optional: Maldon sea salt
Instructions
- Preheat Oven to 350 Degrees
- Prepare an 8×8 Baking Pan with parchment paper and spray the pan and parchment with cooking spray. It’s very important to prevent sticking.
- Mix together the maple syrup, ghee (be sure it’s cooled), egg, vanilla, coconut flour, tapioca flour and salt. It will seem loose, but trust that the coconut flour is like a sponge and it will quickly form a dough you can press in the pan.
- Press your dough into your prepared pan. Poke it lightly with a fork, but do NOT go through the crust completely.
- Bake at 350 degrees for 8 minutes. Take it out and allow it to cool while you make the filling.
- Over medium high heat, in a medium sauce pan, add your ghee, maple syrup, coconut sugar and vanilla. Whisk constantly for about 4-5 minutes.
- Let the mixture come to a low boil for one minute so all the sugar dissolves. It’s very important that you whisk constantly because sugar burns fast.
- The mixture will be slightly thicker than pancake syrup consistency.
- Take it off the heat and add in the vanilla almond milk, pecans and the 1/8 teaspoon of salt. Stir it together and make sure your crust is cool to the touch. It doesn’t have to be cool to room temp, but you should be able to pick up the pan without it being too hot.
- Pour the pecan mixture into the crust and bake at 350 for 15-17 minutes. Note: the mixture will cook down in the oven and reduce. It will still however be a little loose when you take it out. You want to see a lot of bubbling and the pecans to kind of poke through the top.
- Sprinkle the top with the flaked sea salt (if using). I highly recommend this step because it really plays to the sweet and salty nuttiness of these bars.
- Allow the bars to cool on the counter for 1 hour. Transfer to the fridge for at least 2 hours before you cut it.
- Cut them into bars and serve. You can store these in the fridge wrapped in parchment in an air tight container for up to one week. I have not frozen them, but I’d imagine the moisture from freezing wouldn’t be ideal for texture.
Kailey R says
These were freaking awesome and super easy to make. I brought them to a get together and people who don’t even like pecan pie were raving about them. I used butter and whole milk but I don’t think those adjustments changed the flavor profile at all. I also used 2 cups of pecans (not 2.5) which I thoughts was plenty. These bars will definitely be a yearly tradition in my family.
The Clean Eating Couple says
Thank you so much, Kailey!! I’m so glad you liked them! This made my day 🙂
Charity says
I used a smaller pan than called for (gotta use what you have) and thought it was a bust. So I put them back in the fridge overnight and tried them again in the morning and they were ridiculous! The crust part was thicker and softer than the pictures (again, smaller pan), but all of the pecan caramel goodness soaked in and made magic. So use the right size pan or be patient and put them in the fridge overnight.
The Clean Eating Couple says
So glad you liked them, Charity! Thank you so much! They definitely need to cool for at least 2 hours, but I bet if you put it in a smaller pan it needed longer to cook or the cook times were just off because they were so much thicker. Glad you liked them!
Jen says
These are the new family favorite for Thanksgiving and beyond! The recipe is simple to follow and the healthier ingredients make for a perfect gluten free dessert! I was shocked at how easy they were to make. Crusts have always intimidated me but this was simple enough for my kids to make right along side. Nobody at the dinner table guessed these gooey, delicious bars were made with healthier ingredients either. Thanks for yet another winning recipe!
The Clean Eating Couple says
So happy you liked them, Jen! This makes me so happy to hear!
Rajesh says
I tried this for Thanksgiving meal and followed recipe step by step. It turned out perfect and everyone loved it. My favorite part was using ghee in the recipe which our family has been using for long time and they loved eating this. Thank you for sharing the recipe.
The Clean Eating Couple says
So glad you liked them, Rajesh! I really appreciate the nice review!
Becky says
These are INCREDIBLE! I made a batch for Thanksgiving and my husband couldn’t believe these were a “healthier” variation. I can also confirm that these are totally freezeable. I wrapped slices individually in Saran Wrap and then put them in a freezer bag. They’re still totally delicious!
The Clean Eating Couple says
Thanks, Becky!! So glad you liked them and that they froze well!
Cheri says
Made them and absolutely LOVE THEM!!! Will be making them again and again!
The Clean Eating Couple says
Thanks, Cheri! Glad you liked them!
Miriam says
Hi, Could I replace de coconut Flour , I really dont like de flawor of the coconut flour in the finish product. Thanks in Advance
The Clean Eating Couple says
Hi Miriam – No you can’t. We’ve mentioned this a few times in the post. I don’t recommend other flours for the crust, especially almond flour. The crust is a tried and true formula of coconut and tapioca. The tapioca provides a binder along with the egg. You can’t taste the coconut flour, it tastes like a regular buttery crust!
Tobi N says
There are so delicious!! Husband approved as well … it was hard not to eat the whole pan.
Will be a keeper recipe for holidays and easier to have around instead of a whole pie! Will be making this again and again … thank you for the wonderful recipe!!
The Clean Eating Couple says
So glad you both enjoyed! Thanks, Tobi!
Adrienne says
Easy to follow recipe. Used butter and milk in the filling and they were delicious!
The Clean Eating Couple says
Yum! Glad you enjoyed!
Liz kane says
Made this recipe for thanksgiving and they were all gone within minutes! I followed recipe exactly except I used a glass baking dish so instead of baking crust for 8min it took about 11-12min to bake crust. They were so yummy !
Jeanine says
I made the Healthy Pecan Pie Bars for Thanksgiving. Wow. Wow. Wow! They were a huge hit. Absolutely delicious. I made them for my daughter who has some dietary restrictions. I bought a regular pie for the rest of us. Although the pie was good, my daughter had to keep everyone away from her bars!
The Clean Eating Couple says
I’m so happy you liked them, Jeanine! Thank you so much!
Abby says
I totally messed up the consistency when “chopping” the nuts in a food processor that made more of a fine pecan powder, but they still came out yummy! Next time I won’t try to multitask lol. I need to rave about the crust though! It was so good and was my favorite part! I would love more recipes with that as a base!
The Clean Eating Couple says
Definitely chop them with a knife next time, LOL! So glad you liked them though!
Erin says
I’ve made these three times and they were perfect every time! I added vanilla bean ice cream and homemade whipped cream for a more decadent dessert.
I used the pecan filling and put into puff pastry and that was good, just not as fantastic as your shortbread crust.
This is a 5 star recipe.
The Clean Eating Couple says
So glad you liked them! That sounds SO good!
Leona says
Can these be made without crust
The Clean Eating Couple says
I don’t think so.. it’s not really a pecan pie. You’d just have pecans cooked in syrup in a dish. Serving that would make a mess. I don’t recommend trying that
Angel Harrowfield says
Wow!!! these are amazing. Everybody loved them and they are asking for the recipe. Don’t deviate from the recipe and they will be perfect.