Gluten Free Pecan Pie Bars with a Shortbread Crust

These gluten-free pecan bars have everything I love about traditional pecan pie, from the rich caramel filling to the crunchy toasted pecans, but with a buttery shortbread crust instead of pie dough. Dark corn syrup gives the filling a deeper flavor, and the crust gets a quick bake before the filling goes on to keep it from getting soggy.

Pecan pie bars cut into squares on parchment paper, with a small bowl of pecans nearby.

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Skill Level: Intermediate
Flavor Remix: Add a handful of chocolate chips to a cooled filling before baking.
Allergy Watch: Gluten-Free only

I originally tested this recipe with a traditional pie crust, similar to the one I use for my GF apple slab pie. But rolling out gluten-free pie dough was more work than I wanted for a batch of dessert bars. So I went back to my favorite shortbread crust, the one I use in my gluten-free samoas, and paired it with the filling from what I think is the BEST gluten-free pecan pie.

I typically bake gluten-free brownies and bars in an 8x8 pan, but pecan bars are practically made for Thanksgiving dessert tables and Halloween parties. This version fills a standard 9x13 pan, so you have plenty to share.

And if you love that gooey pecan pie filling, the combination with a tender, buttery cookie crust is worth making.

Ingredient Notes

Bowls containing ingredients for gluten-free pecan pie bars: pecans, flour, eggs, powdered sugar, butter, heavy cream, vanilla, baking powder, dark corn syrup, salt, and brown sugar.

Gluten-Free Flour: Use any 1:1 gluten free flour blend with xanthan gum, like Bob's Red Mill 1:1 Flour or King Arthur Measure for Measure.
Dark Corn Syrup: This is what makes my pecan filling special. Light corn syrup works for structure, but dark corn syrup brings a deeper, almost caramel like flavor that pairs beautifully with toasted pecans. I recommend sticking with dark for the best flavor.
Brown Sugar: I prefer light brown sugar in the filling because the dark corn syrup already brings plenty of richness. Dark brown sugar will work, but gives the bars a stronger molasses flavor. The crust also uses a small amount of brown sugar along with powdered sugar.
Butter: Use softened butter for the shortbread crust so it mixes evenly with the flour. The butter for the pecan filling gets melted with the syrup and sugar. I prefer unsalted butter so I can control the salt.
Pecans: Toast the pecans before adding them to the filling to bring out their nutty flavor. Chopped pecans are better than whole halves for bars because they distribute evenly and make the squares easier to cut.
Eggs: The eggs are essential for setting the pecan filling. They turn the syrup mixture into a soft custard that holds together when sliced. I have not tested an egg substitute in this recipe.
Heavy Cream: The cream contributes to the smooth, rich texture of the filling. I have not tested a dairy free replacement for the heavy cream in these bars.

Rectangular container of yellow ice cream with two scoops removed, an ice cream scooper beside it, and a textured cloth in the background.

What to Serve with Pecan Bars

You can turn this from a simple grab-and-go snack to a decadent dessert with vanilla ice cream, whipped cream or caramel sauce.

Frozen Custard

How to Make Gluten-Free Pecan Pie Bars

A step-by-step visual guide for making gluten-free pecan bars You can skip to the recipe for the full written instructions.

Two photos: a bowl of flour next to a bowl of pecans, and a stand mixer bowl containing creamed butter and sugar.

Make the Cookie Crust

Sift together the dry ingredients before adding them to the butter and sugar. The cookie dough will feel wet.

Two side-by-side images showing raw cookie dough spread in a parchment-lined baking pan, and the same dough after being baked.

Par Bake

Don't worry if it looks like there isn't enough dough! The shortbread layer will be thin, but it puffs up slightly as it bakes.

Three-panel image showing a sauce being prepared in a pan: first, melted butter and sugar; second, beaten eggs added; third, chopped pecans stirred in.

Make the Filling

Heat the sugars and dairy elements and whisk until combined. But COOL the filling before adding the eggs- they will scramble!

Two side-by-side views of a rectangular baking pan lined with parchment paper, showing a pecan mixture before and after being baked.

Bake and Cool

Bake for 25 to 30 minutes, until the filling is set. The center should be set rather than liquid, although a slight jiggle is fine.

Let the bars cool completely in the pan before lifting them out using the parchment paper.

Jen's Recipe Notes

Don't add more dough to the crust. It will look surprisingly thin when you first press it into the 9x13 pan. That's intentional. The baking powder gives it a little lift during the initial bake.
Always par bake the shortbread. This is not a step to skip. The pecan filling contains a lot of liquid, and an unbaked crust can become soggy underneath it.
Use dark corn syrup. It has a richer flavor than light corn syrup and gives these bars that deep caramel flavor I love in pecan pie.
Let the syrup mixture cool before adding the eggs. Five minutes off the heat helps prevent little bits of cooked egg in the filling. Whisk the eggs before adding them so they incorporate evenly.
Toast the pecans first. Toasting brings out their flavor, which makes a difference in a dessert with so few dominant ingredients.
Line the pan with parchment paper. Leave enough hanging over the edges to lift out the whole slab. Cutting the bars outside the pan is much more convenient.
Be patient with cooling. The filling continues to firm up as it cools. Cutting the bars while warm can leave you with a gooey mess instead of neat pecan squares. Refrigerate them after cooling if you want especially clean cuts.

Two square pecan pie bars with a crust and a nutty filling.

Make Ahead and Storing

Make Ahead: Bake and cool completely, then refrigerate until you're ready to slice and serve. Making them 1 day in advance also gives the filling plenty of time to firm up.

Storing: Store the cooled bars in an airtight container in the refrigerator for up to 4 days. Let them sit at room temperature briefly before serving if you prefer a softer filling.

Freezing: For longer storage, wrap individual bars and place them in a freezer safe container for up to 2 months. Thaw overnight in the refrigerator before serving. Freezing and thawing may slightly change the filling's texture.

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Recipe Questions

Can I use light corn syrup instead of dark corn syrup?

Yes, light corn syrup will work, but the flavor will be different. Dark corn syrup has a richer flavor that complements the brown sugar and toasted pecans. It's my preference for pecan pie and these bars.

Why is my pecan filling runny?

The most common causes are underbaking and cutting the bars before they have cooled. The eggs need enough time in the oven to set the filling, and the bars need to cool completely before slicing. If they are still soft after cooling, refrigerate them to help the filling firm up.