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
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.
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.
Browned the butter for the streusel instead of cutting it in cold, and the pecan topping went deeply caramelized with an almost toffee richness to it. If your oven runs hot, pull them at 22 minutes because the pecans can tip from perfect to overdone fast. Four stars until I nail the timing on my end, but the direction is right.
Browned butter in the streusel, I hadn't tried that. That toffee caramel thing you're describing, I need to test it now. And yeah, pecan streusel in a hot oven goes from perfect to scorched fast, 22 makes sense.
Made a batch Saturday morning mostly to use up a can of pumpkin puree I had sitting in the pantry, and my daughter (who has been pretty skeptical about every keto baked thing I've attempted) pulled the streusel off the top of her first one and ate it by itself before she even touched the muffin part. That told me more than anything I could say. Only thing I'd note is they run pretty sweet, so I might pull the monkfruit back just slightly next time, but small thing. Good enough that I'm not waiting until fall to make them again.
Ha, that streusel test is better than any review. And yeah, totally fair on the sweetness - 1/3 cup monkfruit instead of the full 1/2 gets you there without changing much else.
Toast the pecans for 5 minutes before mixing the streusel. They stay crunchier on day two and the whole topping smells way more like fall when the muffins come out of the oven. First batch I skipped that step and noticed the difference immediately.
Toasted pecans in the streusel are just better, full stop. That fall smell when they come out is real. I do 350 for 5 minutes and let them cool before mixing in.
My sister is allergic to tree nuts and I want to make these for her this weekend. Can I swap the pecans for pumpkin seeds and still get that crunchy buttery topping, or will it just not work?
Pumpkin seeds work in the streusel, they toast up nicely and still get crunchy. But heads up, the base uses almond flour, which is also a tree nut. If her allergy is severe you'd need to swap that too. Sunflower seed flour is the sub I'd use (same amount, just slightly earthier).
absolutely amazing...so love your channel:)
Ha, these are a fall staple here. Happy you found the channel!
Hi, instead of Pumpkin could I not substitute shredded zucchini? I used to make regular zucchini bread and muffins.
Have them in the freezer and want to use them.
I haven't tried zucchini in this muffin recipe yet. You can try it, but you'll probably need to adjust the flours to get the right batter consistency.
These muffins are hands down the best I have ever made. My whole family enjoys having them in the morning. Thank you for the recipe. It has been a life saver since starting Keto.
Ha, whole family on board is the real test with these. Freeze a batch and reheat at 300 for 10 minutes from frozen. Streusel stays crunchy, microwave kills it.