Two Thanksgivings ago, my aunt showed up with what she kept calling "the best pecan pie ever." It wasn't. The filling was so runny it literally pooled on people's plates, and trying to cut decent slices while it was sliding everywhere turned into this whole thing. Liam sat there watching everyone struggle with their forks and said, "Why don't we just put pecan pie in cupcake papers so it doesn't leak?" You know what? That seven-year-old was onto something. The next weekend we tried making pecan pie cupcakes and yeah, the first batch burned. Second batch was way too sweet.
Why You'll Love These Pecan Pie Cupcakes
Look, I love regular Pecan Pie Cupcakes. But it's kind of a pain, right? You've got to make the crust, worry about it getting soggy, pour in this filling that might not set up right, and half the time someone cuts into it too early and everything just runs all over the place. Last Christmas my brother-in-law sliced into my pecan pie maybe twenty minutes after I took it out of the oven because he "couldn't wait." The filling went everywhere. I'm still annoyed about it.
These pecan pie cupcakes from scratch skip all that drama. The cupcake part soaks up just enough of the pecan filling to stay moist without getting gross and soggy. The filling bakes right into the top and actually sets because it's in smaller amounts instead of one giant pool. You can eat them warm, you can eat them cold from the fridge - doesn't matter, they taste good either way. Made a batch last Sunday, left them on the counter, and Liam grabbed one after dinner. I had one cold the next morning with my coffee. Both were good.
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Ingredients For Pecan Pie Cupcakes
For the Cupcakes:
- 1½ cups all-purpose flour
- 1½ teaspoons baking powder
- ½ teaspoon salt
- ½ cup softened butter
- 1 cup sugar
- 2 large eggs
- 2 teaspoons vanilla extract
- ½ cup whole milk
For the Pecan Pie Filling:
- ¾ cup chopped pecans
- ½ cup light corn syrup
- ⅓ cup packed brown sugar
- 2 tablespoons melted butter
- 1 egg
- 1 teaspoon vanilla extract
- Pinch of salt
For the Brown Sugar Frosting:
- ½ cup butter
- 1 cup packed brown sugar
- ¼ cup milk
- 2½ cups powdered sugar
- 1 teaspoon vanilla extract
Optional Toppings:
- Extra pecan halves
- Caramel drizzle
- Flaky sea salt
Step by Step Method
Prepare Your Cupcake Base
- Heat oven to 350°F and line muffin tin with cupcake papers
- Beat softened butter and sugar for 3 minutes until fluffy and lighter colored
- Add eggs one at a time, beating after each one, then mix in vanilla
- Whisk flour, baking powder, and salt in separate bowl
Build the Cupcake Batter
- Add half the flour mixture to butter mixture and stir
- Pour in milk and mix until combined
- Add remaining flour and mix just until no streaks show
- Fill cupcake liners halfway - not more or they overflow when filling goes in
Make the Gooey Pecan Filling
- Whisk corn syrup, brown sugar, melted butter, egg, vanilla, and salt until smooth
- Stir in chopped pecans until evenly mixed
- Mixture should be thick but still pourable like heavy syrup
- Let it sit while cupcakes are ready for topping
Assemble and Bake
- Spoon about 1 tablespoon pecan filling on top of each cupcake batter
- Don't worry if it looks like too much - it sinks in while baking
- Bake for 20-22 minutes until toothpick in cake part comes out clean
- Pecan topping will still jiggle slightly - that's what you want
Create Brown Sugar Frosting
- Melt butter in saucepan, add brown sugar, and bubble for 2 minutes stirring constantly
- Add milk and bring back to boil, then remove from heat
- Cool for 15 minutes before beating in powdered sugar and vanilla
- Adjust thickness with milk (thinner) or powdered sugar (thicker)
Finish Your Cupcakes
- Let cupcakes cool completely before frosting or it melts and slides off
- Spread or pipe brown sugar frosting on each cupcake
- Top with pecan halves and drizzle with caramel if you want
- Serve at room temperature or cold from fridge - both work great
Equipment For Pecan Pie Cupcakes
- Standard 12-cup muffin tin
- Cupcake liners (paper or foil, doesn't matter)
- Mixing bowls (at least 2)
- Electric hand mixer or stand mixer
- Measuring cups and spoons
- Whisk for the filling
- Medium saucepan for frosting
Pecan Pie Cupcakes Variations
Chocolate Pecan Pie Cupcakes:
- Swap vanilla cupcake batter for chocolate batter
- Add 2 tablespoons cocoa powder to the pecan filling
- Use chocolate ganache instead of brown sugar frosting
- Drizzle with caramel sauce on top
- Tastes like those fancy chocolate pecan pies but easier (Liam's top pick)
Mini Pecan Pie Cupcakes:
- Use mini muffin tin instead of regular size
- Cut baking time down to 12-15 minutes
- Only put about 1 teaspoon filling on each one
- Makes about 36 tiny cupcakes instead of 12 regular
- Perfect for parties where people want to try multiple desserts
Butter Pecan Version:
- Toast pecans in melted butter before mixing into filling
- Add ½ teaspoon butter extract to cupcake batter
- Top with butter pecan frosting instead of brown sugar
- Sprinkle extra toasted pecans on top
- Tastes exactly like butter pecan ice cream but in cupcake form
Old Fashioned Pecan Pie Style:
- Skip the frosting completely
- Double the amount of pecan filling on top of each cupcake
- Serve them warm with vanilla ice cream on the side
- Dust with powdered sugar right before serving
- Way more like eating actual pecan pie, less like a fancy cupcake
Bourbon Pecan (Adults Only):
- Add 2 tablespoons bourbon to the pecan filling
- Use bourbon buttercream instead of brown sugar frosting
- Only make these when kids aren't around
- My husband's favorite - he requests these for his birthday every year
Substitutions
Cupcake Base Options:
- All-purpose flour → Cake flour (lighter texture)
- Whole milk → Buttermilk (tangier flavor)
- Vanilla cupcakes → Yellow cake mix (easier, less from scratch)
- Butter → Oil (moister but less flavor)
Pecan Filling Swaps:
- Light corn syrup → Dark corn syrup (richer taste)
- Corn syrup → Maple syrup (different sweetness)
- Chopped pecans → Pecan halves (looks fancier)
- Pecans → Walnuts (cheaper, similar texture)
Frosting Alternatives:
- Brown sugar frosting → Maple buttercream (easier to make)
- Homemade → Cream cheese frosting (tangier)
- Butter frosting → Caramel frosting (sweeter)
- Full frosting → Just whipped cream (lighter option)
Sugar Changes:
- Brown sugar → Dark brown sugar (deeper molasses flavor)
- White sugar → Coconut sugar (less sweet)
- Regular → Half honey (stickier filling)
Storage Tips
Room Temperature (2 days):
- Keep in airtight container on counter
- They're fine at room temperature because of the corn syrup in filling
- Actually taste better day two after flavors settle
- Don't stack them or frosting gets smashed
In the Fridge (5-6 days):
- Store in covered container once completely cool
- Bring to room temperature before eating for best taste
- Or eat them cold - some people prefer it that way
- Frosting gets firmer when cold but softens up after 10 minutes out
Freezing (Up to 2 months):
- Freeze unfrosted cupcakes in freezer bags
- Thaw overnight in fridge before frosting
- Make frosting fresh when you're ready to serve
- Frosted ones get weird and watery when thawed
Make-Ahead Tips:
- Bake cupcakes up to 2 days ahead and store covered
- Make frosting day-of for best texture
- You can also freeze just the baked Pecan Pie Cupcakes and frost later
- Pecan filling keeps them moist even after a few days
Top Tip
- Don't Overfill the Liners: Only fill the cupcake liners halfway before you add pecan filling. Yeah, it looks like not enough. It's not. First batch I made, I filled them almost to the top thinking more was better. Half of them overflowed in the oven and made this burnt pecan disaster all over my muffin tin. Took me twenty minutes scrubbing that mess off.
- Let the Frosting Cool: That brown sugar frosting needs to sit off the heat for at least fifteen minutes. Maybe twenty. If you try spreading it while it's still warm, it's too runny and slides right off the Pecan Pie Cupcakes. I've done this twice because I was rushing and didn't want to wait. Both times I had to scrape everything off, wait longer, then frost them all over again.
- Toast the Pecans: Throw them in a dry pan for five minutes. Shaking every minute or so. They go from bland and boring to buttery and kind of caramel-y. Way better. But don't walk away from the stove while they're toasting - they burn really fast. I've torched two whole batches because I left them to answer my phone.
FAQ
Is pecan pie better at room temperature or cold?
Depends who you ask. I like these at room temperature because the frosting is softer and everything tastes better. Liam likes them straight from the fridge because he says the filling gets "more chewy" that way. My husband eats them however they come out and doesn't care either way. Try both and see what you like. The frosting does get pretty hard when cold though, so if you want it soft, let them sit out for fifteen minutes first.
Will pecan pie still be jiggly after baking?
Yeah, the pecan stuff on top should still wobble when you take them out. That's how it's supposed to look. It firms up while they cool. If you wait until it's totally solid in the oven, the Pecan Pie Cupcakes underneath will be dry. I used to overbake them because the jiggle freaked me out - thought they weren't done. They were done.
Can I make pecan pie cupcakes using cake mix?
Sure. Use a box of yellow cake mix or butter cake mix instead of making batter from scratch. Follow what the box says but only fill liners halfway, then put the homemade pecan filling on top before baking. Still takes about 20-22 minutes. I've done this when I was running late and they came out fine. Not quite as good as from scratch but way easier. Most people couldn't tell anyway.
What makes these different from Pecan Pie Cupcakes?
Pecan Pie Cupcakes have pecans mixed into the cake and butter pecan frosting all over. These have regular vanilla cake with pecan pie filling on top, so you get that gooey pecan pie texture instead of just pecan taste. More like eating real pecan pie that happens to be shaped like a cupcake. Different thing completely.
Just Make These Already
That's everything I've figured out about these after making them probably a hundred times. These pecan pie cupcakes work for Thanksgiving, sure, but also for random weeknights when you want something sweet, or when you need to bring dessert somewhere and want people to be impressed without actually spending your whole day baking. Nobody fights over who got more pecans because they're all the same.
Need more desserts that don't eat up your whole afternoon? Try our Easy Homemade German Chocolate Cake Roll - looks way fancier than it actually is to make. Our Easy Nun Puffs Recipe ready in 30 minutes is what I make when people are coming over and I forgot about dessert until the last minute. And if your kids are Harry Potter fans, our Easy Harry Potter Butterbeer Cupcakes get eaten faster than anything else I've ever baked.
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Pairing
These are my favorite dishes to serve with Pecan Pie Cupcakes
Pecan Pie Cupcakes
Equipment
- 1 12-cup muffin tin (standard size)
- 12 Cupcake liners (paper or foil)
- 2 Mixing bowls (separate wet/dry)
- 1 Electric mixer (hand or stand)
- 1 Whisk (for filling)
- 1 Medium saucepan (for frosting)
Ingredients
For the Cupcakes
- 1½ cups all-purpose flour
- 1½ teaspoon baking powder
- ½ teaspoon salt
- ½ cup butter - softened
- 1 cup sugar
- 2 large eggs
- 2 teaspoon vanilla extract
- ½ cup whole milk
For the Pecan Pie Filling
- ¾ cup chopped pecans - toasted for best flavor
- ½ cup light corn syrup - or dark for richer taste
- ⅓ cup brown sugar - packed
- 2 tablespoon butter - melted
- 1 large egg
- 1 teaspoon vanilla extract
- 1 pinch salt
For the Brown Sugar Frosting
- ½ cup butter
- 1 cup brown sugar - packed
- ¼ cup milk - whole or 2%
- 2½ cups powdered sugar
- 1 teaspoon vanilla extract
Optional Toppings
- pecan halves - garnish
- caramel sauce - drizzle
- flaky sea salt - optional
Instructions
- Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with cupcake liners and gather ingredients.
- Beat butter and sugar until light and fluffy. Add eggs and vanilla, then mix in flour, baking powder, salt, and milk until smooth. Fill cupcake liners halfway.
- Whisk corn syrup, brown sugar, melted butter, egg, vanilla, and salt. Stir in chopped pecans until evenly coated.
- Spoon 1 tablespoon of pecan filling over each cupcake. Bake 20-22 minutes until a toothpick in the cake part comes out clean and the pecan layer is slightly jiggly. Cool completely.
- Make brown sugar frosting, spread or pipe onto cooled cupcakes, and top with pecan halves, caramel drizzle, or sea salt if desired.
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