Keto Pumpkin Pecan Muffins
Published November 1, 2020 • Updated February 27, 2026
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Fluffy low carb pumpkin muffins loaded with fall spices and topped with a buttery pecan streusel that my family eats straight off the top.
I started making these keto pumpkin pecan muffins because I had half a can of pumpkin puree and a bag of pecans that needed a purpose. Four batches later, they became a fall staple in my house. One of my readers made a batch for his family and his daughter pulled the streusel off the top of her first muffin and ate it by itself before she even touched the rest. That told me the topping formula was right.
The secret is toasting the pecans first. I do 350°F for about 5 minutes, let them cool, then mix them into the streusel. The crunch holds up even on day two, and the whole kitchen smells like fall when you pull the muffins out. Skip that step and you will notice the difference by the next morning.
The base is almond flour with a couple tablespoons of coconut flour to soak up the extra moisture from the pumpkin puree. I use pumpkin pie spice (not just cinnamon) because I want the full warm flavor, not a one-note muffin. If you are into pumpkin baking, my pumpkin bread uses a similar spice base, and my pumpkin cream cheese muffins go a completely different direction with a cream cheese filling.
One thing I have adjusted since the original recipe: I pull the monkfruit sweetener back to about 1/3 cup instead of 1/2. The pumpkin and spices carry enough sweetness on their own, and the streusel adds another layer on top. If you find sweet baked goods overwhelming, start lower. You will not miss it.
These bake at 325°F, which is lower than most muffin recipes. I do this on purpose. The lower temperature lets the muffins bake through without the streusel burning. At 350°F, the topping darkens before the centers are set. Give them the full 30-35 minutes and check with a toothpick.
For storage, I keep them in an airtight container at room temperature for up to three days. They also freeze well (individually wrapped) for up to three months. Reheat from frozen in a 300°F oven for about 10 minutes. The microwave works but the streusel goes soft. If you are building out a low carb muffin rotation, my lemon blueberry muffins and strawberry muffins are good for warmer months, and my apple fritters are another fall favorite.
I have got a whole muffin collection at this point. My lemon poppyseed muffins are the spring version of these, and my chocolate zucchini muffins use up extra produce the same way these use pumpkin.
Keto Pumpkin Pecan Muffins Ingredients
2 cup almond flour -
1 cup 100% pumpkin puree
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4 eggs
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1/2 cup golden monkfruit sweetener, or brown Swerve
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1/2 cup heavy cream
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2 tablespoons coconut flour
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1 tablespoon pumpkin pie spice
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2 teaspoons baking powder
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¼ teaspoon of salt
Pecan Streusel Ingredients
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1/3 cup almond flour
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1/4 cup golden monkfruit sweetener, or brown Swerve
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1/4 cup crushed pecans
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3 tablespoons cold butter, cut into cubes
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2 tablespoons coconut flour
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1 teaspoon cinnamon
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1/4 teaspoon salt
Step by Step Instructions
Step by Step Instructions
Preheat oven
Preheat oven to 325 degrees. Place muffin liners in a 12 cup muffin pan.
Add pumpkin pecan mixture
In a large bowl, add all the muffin batter ingredients and mix until combined.
Add mixture to muffin pan
Scoop mixture into each muffin liner, filling almost to the top leaving room to add the streusel.
Add pecan streusel mixture
To make the pecan streusel, add all the ingredients to a small bowl and cut in butter using a fork or pastry blender until coarse crumbles form.
Apply streusel to the top
Evenly distribute streusel on top of each muffin.
Bake it
Bake at 325 degrees for about 30-35 minutes or until spongy. Remove from oven and let cool.
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
Should I toast the pecans before making the streusel?
I toast mine at 350°F for about 5 minutes and let them cool before mixing them into the streusel. The difference is real, especially on day two. Without toasting, the pecans soften faster and you lose that crunch. My first batch I skipped it and I could tell right away.
Can I make these nut-free for someone with a tree nut allergy?
I have walked through this with a reader. Pumpkin seeds work as the pecan swap in the streusel and they toast up nicely. But the muffin base uses almond flour, which is also a tree nut. For a severe allergy, I would swap that to sunflower seed flour (same amount). It runs slightly earthier in flavor but the texture holds.
Can I make mini muffins with this recipe?
I have not tested a mini version yet, but the batter would work in a mini muffin pan. I would cut the bake time to about 15-18 minutes at the same 325°F and check early with a toothpick. The streusel pieces need to be smaller so they do not overpower the mini tops.
How do I reheat these from frozen?
I wrap each muffin individually before freezing, then reheat straight from frozen in a 300°F oven for about 10 minutes. The oven is key. Microwaving works if you are in a rush, but the streusel goes soft. I have tested both ways and the oven wins every time.
Why do these bake at 325°F instead of 350°F?
I tested both temperatures when I first developed this recipe. At 350°F, the pecan streusel darkens and starts to burn around the edges before the muffin centers are fully set. The lower 325°F gives the inside enough time to bake through. With low carb batters (almond flour holds moisture differently than wheat flour), you need that extra time at a gentler heat.
Can I use less sweetener? These seem pretty sweet.
I have started pulling the monkfruit back to about 1/3 cup instead of the full 1/2 cup. The pumpkin puree and spices carry more sweetness than you would expect, especially when you are baking keto and already using a concentrated sweetener. Start with 1/3 cup and taste the batter before you commit.
How should I store leftover muffins?
I keep mine in an airtight container at room temperature for up to three days. After that the streusel starts losing its crunch. For longer storage, I freeze them individually wrapped for up to three months. They hold up well from frozen if you reheat in the oven instead of the microwave.
Can I make these dairy-free?
I would swap the heavy cream for full-fat coconut cream (not coconut milk, it is too thin). For the streusel butter, coconut oil works but you need it cold and firm so it cuts into crumbles the same way. I have done the coconut cream swap and the muffins were slightly less rich but still good.
If you need a muffin that screams Fall is here, this is it. This big fluffy muffin is made with pumpkin and topped with a buttery, sweet & salty streusel. I’m pretty sure these muffins and coffee were meant to be consumed together because they’re a match made in heaven on a cool, crisp Autumn morning.
I like to enjoy these pumpkin muffins in the morning or when I’m running late to work. They’re easy to pop in my bag or into my kids’ lunch box and the macros keep me full until my next meal.
Been stashing batches in the freezer. My son is 16 and won't touch anything he knows is keto. Thawed one Thursday, streusel still crunched. Gone by Friday.
Does the two tablespoons of coconut flour actually do anything? I left it out on my second batch and the crumb collapsed. Hadn't eaten a muffin in over a year before these, and now I can't stop.
Dina, your second batch proved it. Coconut flour absorbs the moisture from the pumpkin and eggs in a way almond flour can't, so pull it and the crumb just doesn't hold. I've had that exact collapse happen in testing.
4.5 net carbs stopped me mid-scroll. Made a batch Sunday and the crumb is way more tender than most almond flour muffins I've made. One thing I'd flag: the 2 tablespoons of coconut flour is a precise call, don't bump it up. Second batch I went to 3 tablespoons thinking more structure, and the texture turned grainy and dry pretty fast. Back at 2 and these are legitimately good.
Trust the 325. I went up to 350 my first batch (every muffin recipe I own calls for it) and the tops browned while the centers were still raw. Dropped back down and they finally set right. That lower temp is why these have actual muffin texture instead of the dense, dry thing almond flour does at higher heat.
The streusel gets you first at 350. Took three batches to commit to 325.
Why isn't heavy cream in every keto muffin?
Fat keeps the crumb tender in a way that coconut milk just doesn't. I put it in almost everything now.
Cold from the fridge and still moist on day four. Almond flour baked goods never do that, and I'm genuinely annoyed it took me this long to find this recipe. Two dozen in the freezer. Thirty seconds in the microwave.
Heavy cream is what makes day four good. And when you pull those from the freezer, try 300 for about 10 minutes instead. Microwave kills the streusel.
There was a diner near where I grew up that made pumpkin muffins, the kind with that deep warm spice that hits you before you even bite in. Filed them under 'gone forever' when I went keto. These aren't gone.
The 'not gone' is what I was going for with this one. That smell is a full tablespoon of pumpkin pie spice.
Drain your pumpkin puree first. Way less dense.
Kendra, I started doing this after a batch came out softer than I wanted. Paper towels for about 10 minutes before measuring.
Swapped the golden monkfruit for brown Swerve in the streusel and that depth in the pecan topping is why I'm on batch three in two weeks.
Brown Swerve does something to that pecan streusel the golden monkfruit just can't get to. Three batches in two weeks tracks.
Six batches in and I finally cracked the streusel: brown Swerve instead of golden monkfruit, and the pecans get almost crunchy-sticky. The muffin itself is solid but that top is the whole reason I keep making these.
Six batches means you get to have opinions. If you haven't toasted the pecans yet, try 5 minutes at 350 and let them cool first. The crunchy-sticky holds up even longer.
Browned the butter for the streusel before cutting it in and the pecans came out almost candied (that toffee smell about knocked me over when I opened the oven). Not going back to the cold butter method.
That toffee smell is getting me just reading this. Haven't browned the butter in this streusel yet but now I have to.
My grandmother made pumpkin muffins every October and I figured that was just gone when I went keto. That pecan streusel took me straight back to her kitchen. Double batch this weekend.
That streusel gets me every time too. Freeze half of the double batch individually wrapped - 300 for 10 minutes straight from frozen and the streusel holds up. Microwave ruins it.
Brought these to a book club last weekend and the pecan streusel had people picking pieces off the tray before I even set them down. Someone asked if they were from a bakery, which I didn't expect since I'm still pretty new to keto baking. Told them it was almond flour and got some skeptical looks until I pulled up the recipe on my phone. Only thing I'd change is dialing back the sweetness a touch, but that's just me.
The bakery comment is the one. And on the sweetness, I've started pulling it back to 1/3 cup instead of the full 1/2. The pumpkin carries more than you'd expect.
Went in skeptical because I've made enough dense almond flour muffins to stop expecting much. The crumb was actually fluffy, and the pecan streusel held its crunch all the way through cooling, which is more than I can say for every other keto muffin I've tried.
The toasted pecans make that crunch last. I do five minutes at 350, let them cool first. The difference shows up on day two.
Fourth batch since fall and I'm not waiting until October to make them again. The streusel keeps pulling me back (I've started making extra just for that part). 325 degrees is right for these, don't push it higher or the tops dry out.
Making extra streusel just to eat straight is honestly the right call. And 325 is the number, I pushed to 340 once just to see and the tops went from golden to dried out in about two minutes flat.