Keto Pecan Pie Muffins
Published October 24, 2021 • Updated March 13, 2026
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These pecan pie muffins are my go-to when I want that warm, gooey filling without making a whole pie. Each one has a caramel-like center so soft you eat it with a fork.
I started making keto pecan pie muffins back in 2018 when I wanted something that tasted like Thanksgiving morning but took 20 minutes and dirtied one bowl. The idea was simple: take everything I love about that warm, buttery filling and bake it in a muffin tin instead of a pie shell. No crust, no rolling, no blind baking. Just pecans, brown sugar, butter, and a few minutes in the oven.
The gooey center is the whole point of this recipe. There’s no baking powder or baking soda in the batter, and that’s intentional. I don’t want these to rise like a regular muffin. I want them dense and fudgy, like you’re eating filling straight from the tin. When you pull one apart warm, the center has this soft, almost molten quality. The edges crisp up golden and the inside stays soft.
What makes these work on keto is how few ingredients you need. Almond flour and coconut flour replace regular flour, sugar-free brown sugar handles the sweetness, and the rest is just butter, eggs, pecans, and salt. Everything goes into one bowl with an electric mixer. If you like simple keto baking projects, my keto strawberry muffins and keto lemon poppyseed muffins are the same kind of one-bowl recipe.
I’ve tested a few variations over the years. Browned butter gives the whole thing a deeper caramel flavor. One of my readers, Paige, tried it and said the filling tasted even more like the real thing. I haven’t done it with this recipe yet, but I’m doing it next batch. Unsweetened chocolate chips stirred into the batter add a nice contrast to the buttery filling (about 2 tablespoons per batch, sugar-free to keep carbs down). For dairy-free, solid vegan butter works well. Miyoko’s or Earth Balance sticks are what I’d recommend. Avoid the spreadable kind because it has more water content and makes the center looser instead of gooey. Ghee is another option if lactose is the issue but dairy fat is fine.
The thing I hear most from readers is that these don’t taste like a “keto version” of something. They just taste like warm filling in a different shape. Beki hid a secret batch in her garage freezer so her kids wouldn’t eat them all. RhondaD’s husband ate nearly a whole batch by himself. If you’re sharing, double the recipe.
These keep well as a low carb breakfast or afternoon snack. I make a batch on Sunday and grab one each morning with coffee. For more keto baking, try my keto pumpkin bread.
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Ingredients
1 cup sugar free brown sugar -
1/2 cup almond flour
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1 tablespoons coconut flour
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2 cups chopped pecans
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1/2 teaspoon salt
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2/3 cup unsalted butter, softened
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2 eggs
Step by Step Instructions
Step by Step Instructions
Preheat oven & line muffin tin
Preheat oven to 350 degrees and line muffin pan with muffin liners. Spray each liner with cooking spray to prevent sticking.
Mix dry ingredients
Add sugar free brown sugar, almond flour, coconut flour, chopped pecans and salt to a large bowl. Whisk until evenly combined.
Scoop into muffin liner
Fill each liner with pecan pie batter until it reaches the top. Top with a whole pecan if desired.
Nutrition disclaimer
The nutrition information provided is an estimate and is for informational purposes only. I am a Doctor of Pharmacy (Pharm.D.); however, this content is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always consult your physician or other qualified health provider before making any lifestyle changes or beginning a new nutrition program.
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Get My Macros + Recipes →Frequently Asked Questions
Why don't these muffins rise like regular muffins?
I leave out baking powder and baking soda on purpose. I want these dense and fudgy, like you're eating the filling of a pie instead of a fluffy muffin. The first time I made them, I actually added baking powder and they puffed up into something that completely lost the gooey center. I took that out and never looked back.
Can I make these dairy-free?
I've had readers use solid vegan butter with great results. I'd go with Miyoko's or Earth Balance sticks rather than the spreadable kind. Spreadable vegan butters have more water in them, which makes the center looser instead of gooey. Ghee works too if dairy fat is fine but lactose is the issue. The center still pulls apart the same way with any of these swaps.
Why are my muffins crumbling — is that normal?
They're supposed to be a little crumbly when they're warm. That's the nature of having a gooey center with no leavening. I eat the first one with a fork every single time. If you want them firmer, give them a full 10 minutes to cool in the tin before you touch them. Once they set, the liner peels off clean and they hold together. If they're crumbling even after cooling, my guess is the butter wasn't soft enough when you mixed it.
Can I use browned butter instead of softened butter?
I haven't tested this myself yet, but one of my readers browned the butter and said the whole muffin got a deeper caramel flavor. I'm doing it next batch. If you try it, make sure you cool the browned butter back to room temperature before mixing it in. Hot butter will cook the eggs and change the texture completely.
How do I reheat these without losing the gooey center?
Microwave, 15-20 seconds. That's what I do every time. I've tried the oven and it dries them out. The microwave brings back that warm, soft center without toughening the outside. From frozen, I thaw overnight in the fridge and then microwave from cold.
Can I add chocolate chips to the batter?
I stir in a handful of unsweetened chocolate chips sometimes, and they add a nice contrast to the buttery filling. I use about 2 tablespoons per batch. Just make sure they're sugar-free if you're tracking carbs closely, because regular chocolate chips will push the net count up fast.
Can I substitute the almond flour with another type of flour?
I use almond flour to keep the carb count low, but sunflower seed flour works if you need a nut-free option. The texture shifts a little (slightly grittier), but the gooey center still comes through. I wouldn't use coconut flour as a 1:1 swap here. It absorbs way more liquid than almond flour and my test batch came out dry and dense in the wrong way.
What can I use instead of sugar-free brown sugar?
I've tested this with granulated erythritol and monk fruit blends, and both work. The brown sugar version gives you more of that caramel depth, so I'd look for a brown sugar blend specifically (Swerve Brown and Lakanto Golden both work for me). I've heard good things about allulose and BochaSweet for browning behavior, but I haven't tested those in this recipe yet.
Batch six and I finally got the cooling time right. Pull them too early and the liner tears and the whole thing collapses, which I did the first three or four times. Give them 10 full minutes and that gooey pecan center holds together on the first bite. Been running these on repeat since I got back into keto this month, 1.3 net carbs and they shut down every craving.
That's a lot of muffins to learn the hard way. Ten minutes is right. Rush it and the liner peels back and takes half the bottom with it.
Browned the butter instead of using it softened and the whole muffin got this deeper caramel flavor that made the pecan filling taste even more like the real thing.
Oh that's a good call. Browned butter and pecans are made for each other. I haven't done it with this one but I'm doing it next batch.
I'm putting together a little brunch for Saturday and these jumped out at me immediately (pecan pie is basically my weakness). My thing is always to do as much prep Thursday or Friday so Saturday morning actually stays calm, which means I need to figure out how these hold up when made ahead. My main concern is that gooey pecan center, because that kind of filling can get weird after it's been cold and comes back to room temp. Can I bake a full batch a day or two out and just leave them covered on the counter, or do they need to go in the fridge? And if refrigerating is the way, do you warm them in the oven to bring that texture back or is the microwave okay? Also planning to double the batch anyway, so does the filling survive freezing or does it get dense and lose that whole melty thing?
Counter is fine for 2 days, just keep them airtight. The gooey center holds up better than you'd think. Microwave over oven to reheat, 15-20 seconds is enough. Freezing works too, I do it all the time. Up to 2 months. Thaw overnight in the fridge and microwave from cold.
My husband has a pretty serious dairy allergy, so I'd need to swap out the butter. Would vegan butter work, or does the fat content matter too much for that gooey center?
Vegan butter works fine here. The fat content is close enough that the center still gets that gooey pull. I'd use one that's solid at room temperature (Miyoko's or Earth Balance sticks) rather than the spreadable kind - those have more water and can make it looser.
Gone Keto on the advise of my Endocrinologist and was doing well but feeling a little down missing out whilst everyone was indulging in Christmas treats. Then I found you Annie. These muffins are ridiculously good! Forget the Keto side they are my dream in a muffin. My kids and husband demolished the first batch ( I got one) so I waited until they all went out for the day and made myself a secret batch. In the garage 'Meat' freezer where I can grab one each day for my work lunch box on the way out when I feel the need. Thank you so much. Your recipes, videos and website are a life saver.
Just made these for my hubby and they smell HEAVENLY...but, I think I didn't let my butter soften enough because they seem a little juicy.....lol Totally my bad. I will make sure to soften the butter completely next time. He has not tried them yet but we shall see. I am loving your recipe site.
Ha, that's usually it. Soft butter is what gives these their gooey center so if it's too firm the fat doesn't distribute the same way. They'll probably still taste great though, the pecans and brown sugar carry a lot.
Great recipe. We really loved them. Easy to prepare. Will definitely make these again. Thank you.
The caramel center is what keeps me coming back to this one. Try stirring in a couple tablespoons of sugar-free chocolate chips next batch. Really good contrast.
Fabulous! Been trying lots of keto muffins, my fav so far! Yes a bit crumbly… how about some xanthum ?
Xanthan gum may help with the crumbling. I'm glad you enjoy them!
My husband is a sweets lover and these were just what the doctor ordered! These are so good, my husband ate almost one whole batch by himself. I'm definitely making these again, possibly in different flavors!
Ha, almost one whole batch is basically the limit before I have to start hiding them. Walnuts are good too if you want to change it up, or throw some unsweetened chocolate chips in the center.